Diff of the two buildlogs: -- --- b1/build.log 2025-11-01 14:37:53.530466298 +0000 +++ b2/build.log 2025-11-01 15:18:05.044743237 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 1 01:37:14 -12 2025 -I: pbuilder-time-stamp: 1762004234 +I: Current time: Sat Dec 5 11:00:58 +14 2026 +I: pbuilder-time-stamp: 1796418058 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -34,53 +34,85 @@ dpkg-source: info: applying script-shebang-line.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3677769/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 4 21:01 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1051b669ed8141858b28731a255ac768' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3677769' - PS1='# ' - PS2='> ' + INVOCATION_ID=ed26184d525549439d2291938d1b9807 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=141509 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3nzuJkv3/pbuilderrc_5Ebf --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3nzuJkv3/b1 --logfile b1/build.log gromacs_2025.3-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3nzuJkv3/pbuilderrc_2VjR --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3nzuJkv3/b2 --logfile b2/build.log gromacs_2025.3-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3677769/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -93,7 +125,7 @@ Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19862 files and directories currently installed.) +(Reading database ... 19869 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -542,10 +574,10 @@ Get: 344 http://deb.debian.org/debian forky/main amd64 texlive-latex-recommended all 2025.20250927-4 [8509 kB] Get: 345 http://deb.debian.org/debian forky/main amd64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 346 http://deb.debian.org/debian forky/main amd64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] -Fetched 468 MB in 25s (18.9 MB/s) +Fetched 468 MB in 16s (29.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19862 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19869 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package poppler-data. @@ -561,7 +593,7 @@ Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20730 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20737 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -597,7 +629,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21745 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21752 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. @@ -1658,8 +1690,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 1 13:40:59 UTC 2025. -Universal Time is now: Sat Nov 1 13:40:59 UTC 2025. +Local time is now: Fri Dec 4 21:05:13 UTC 2026. +Universal Time is now: Fri Dec 4 21:05:13 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... @@ -1989,7 +2021,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gromacs-2025.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2025.3-1_source.changes +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gromacs-2025.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gromacs_2025.3-1_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2025.3-1 dpkg-buildpackage: info: source distribution unstable @@ -2199,8 +2235,8 @@ -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex --- Configuring done (33.3s) --- Generating done (1.0s) +-- Configuring done (45.5s) +-- Generating done (1.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.3/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2025.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_DOUBLE=ON) @@ -2398,8 +2434,8 @@ -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex --- Configuring done (15.6s) --- Generating done (1.5s) +-- Configuring done (37.9s) +-- Generating done (1.0s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.3/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) @@ -2621,8 +2657,8 @@ -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex --- Configuring done (23.7s) --- Generating done (1.0s) +-- Configuring done (30.9s) +-- Generating done (1.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.3/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) @@ -2834,12 +2870,12 @@ -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex --- Configuring done (26.7s) --- Generating done (1.4s) +-- Configuring done (37.3s) +-- Generating done (2.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.3/build/mpi-dp touch configure-stamp dh_testdir -/usr/bin/make -j40 -C build/basic +/usr/bin/make -j42 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.3/build/basic//CMakeFiles/progress.marks @@ -2852,27 +2888,27 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' @@ -2886,153 +2922,153 @@ make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp +cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/lmfit/lmmin.cpp -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwlzh.c -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_float.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build +cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwt.c +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractoption.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/coder.c +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/filenameoptionmanager.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/bcast.cpp +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/eigensolver.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/barrier.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/gmx_arpack.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/p2p_send_recv.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/bcast.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 0%] Built target internal_rpc_xdr -cd 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvardeps.cpp -[ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvargrid.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/topology.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 0%] Built target lmfit_objlib -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/list.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarmodule.cpp +[ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparams.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/type.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparse.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_init.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_io.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/topology.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/list.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 0%] Built target mdrun_objlib +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/type.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/numa_malloc.cpp @@ -3049,6 +3085,8 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 0%] Built target scanner +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' @@ -3065,12 +3103,8 @@ make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 4%] Built target thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 4%] Built target scanner -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 6%] Built target tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 6%] Built target options -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend @@ -3085,17 +3119,17 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidesimulationworkload.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/findallgputasks.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/findallgputasks.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/reportgpuusage.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src 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/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/usergpuids.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/expandedensembleelement.cpp @@ -3117,10 +3151,12 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 8%] Built target taskassignment +[ 8%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 12%] Built target taskassignment +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 14%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' @@ -3950,58 +3986,58 @@ /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend 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/build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build +/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT share/template/CMakeFiles/template.dir/template.cpp.o -MF CMakeFiles/template.dir/template.cpp.o.d -o CMakeFiles/template.dir/template.cpp.o -c /build/reproducible-path/gromacs-2025.3/share/template/template.cpp +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include 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CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/resourceassignment.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/box.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/gmxcalculatorcpu.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/integrator.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/interactions.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/molecules.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/mdsignals.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/nbnxmsetuphelpers.cpp -/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/particlesequencer.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include 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/build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/transformations.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include 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-DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/convertGmxToNblib.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/util/setup.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/system.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/version.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/workflow.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tpr.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT share/template/CMakeFiles/template.dir/template.cpp.o -MF CMakeFiles/template.dir/template.cpp.o.d -o CMakeFiles/template.dir/template.cpp.o -c /build/reproducible-path/gromacs-2025.3/share/template/template.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 93%] Built target gmx @@ -4026,8 +4062,8 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/methane-water-integration.cpp @@ -4044,7 +4080,7 @@ make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -j40 -C build/basic-dp +/usr/bin/make -j42 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2025.3/build/basic-dp//CMakeFiles/progress.marks @@ -4054,13 +4090,13 @@ /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend @@ -4069,177 +4105,177 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build +/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/energyterm.cpp -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/errhandler.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_malloc.cpp +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwlzh.c +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_float.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/atomic.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwt.c +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractsection.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/lock.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/coder.c /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/errhandler.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/basicoptions.cpp +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvar.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/pthreads.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/dict.c +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/behaviorcollection.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/eigensolver.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvar_neuralnetworkcompute.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/alltoall.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/fixpoint.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/mdrun.cpp -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/p2p_protocol.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/gmx.cpp -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/atomic.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/topology.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_protein.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_rotations.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_init.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/topology.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' [ 2%] Built target energyanalysis -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/warnmalloc.c -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_volmaps.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvardeps.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +[ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvargrid.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarmodule.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparams.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' [ 2%] Built target mdrun_objlib -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d 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-I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/tng_io.c -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include 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-Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/once.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparams.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparse.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' [ 2%] Built target lmfit_objlib -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/scan.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT 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/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_system.cpp @@ -4254,11 +4290,7 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 6%] Built target thread_mpi -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 6%] Built target scanner -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 6%] Built target linearalgebra +[ 2%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" @@ -4272,36 +4304,40 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 8%] Built target tng_io_obj +[ 2%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 8%] Built target options +[ 6%] Built target thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 10%] Built target pulling +[ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidesimulationworkload.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/findallgputasks.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/reportgpuusage.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/resourcedivision.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/taskassignment.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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/build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include 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CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/checkpointhelper.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/compositesimulatorelement.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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-Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/constraintelement.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/domdechelper.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp @@ -4322,9 +4358,9 @@ cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 14%] Built target colvars_objlib +[ 10%] Built target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 14%] Built target taskassignment +[ 14%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend @@ -5156,43 +5192,43 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/resourceassignment.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/box.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/exceptions.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/gmxapi.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/md.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/mdsignals.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/particlesequencer.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/nbnxmsetuphelpers.cpp cd 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/system.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/particlesequencer.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 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-Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tpr.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/topologyhelpers.cpp +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/calculator.cpp @@ -5220,216782 +5256,27 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/methane-water-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build -/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/argon-forces-integration.cpp -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.3/build/basic-dp/lib -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp -/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY 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'/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build -/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build -/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build -/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" 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-I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/tests/pairlist.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build -/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include 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'/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build -/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build -/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" 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plumed_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include 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/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 -cd 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 65%] Built target domdec-mpi-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" -[ 65%] Built target taskassignment-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include 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'/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/compat/tests/pointers.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 66%] Built target domdec-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/fixedcapacityvector.cpp -/usr/bin/c++ -g -O2 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../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 69%] Built target mdrun_test_infrastructure -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/tests/indexutil.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/swapcoords.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/tests/settimestep.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 78%] Built target pdb2gmx3-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/tpitest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/constantacceleration.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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'/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem 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/build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/updategroups.cpp -[ 79%] Built target options-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/updategroupscog.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 79%] Built target mdrun-modules-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/normalmodes.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/replicaexchange_equivalence.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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-DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/pmetest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/simple_mdrun.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/periodicactions.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests 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src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd 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/build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/expandedensemble.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/pull.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/pull_rotation.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 -[ 79%] Built target tool-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include 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'/build/reproducible-path/gromacs-2025.3/build/basic' -[ 80%] Built target mdrun-tpi-test -[ 80%] Built target mdrun-output-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/virtualsites.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" 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"CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 82%] Built target utility-test -/usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd 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directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/runner.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 82%] Built target mdrun-io-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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"CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 84%] Built target mdrun-multisim-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/topology.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 84%] Built target coordinateio-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/virials.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/gmxcalculator.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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-isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 87%] Built target workflow-details-test -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 87%] Built target mdrun-mpi-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/typetests.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp -[ 87%] Built target mdrun-coordination-coupling-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/cmdlineparser.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 87%] Built target mdrun-coordination-basic-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests/threadaffinity.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/transformations.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 88%] Built target nblib-tpr-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/filenm.cpp -/usr/bin/c++ -g -O2 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../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 88%] Built target mdrun-coordination-constraints-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 -[ 88%] Built target nblib-util-test -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests/helpformat.cpp -[ 88%] Built target mdrun-rotation-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests/helpmanager.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests/helpwritercontext.cpp -/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests/analysisdata.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 88%] Built target gmxapi-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests/arraydata.cpp -/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 89%] Built target nblib-integrator-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 89%] Built target nblib-integration-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trajectory.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 91%] Built target mdrunutility-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/unionfind.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 92%] Built target onlinehelp-test -[ 92%] Built target mdrunutility-mpi-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 93%] Built target mdrun-fep-test -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 93%] Built target plumed_md-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 94%] Built target mdrun-multisim-replex-equivalence-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 94%] Built target mdrun-pull-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 96%] Built target commandline-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 97%] Built target math-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 97%] Built target analysisdata-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" 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/build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 97%] Built target nblib-tests -cd /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 98%] Built target nblib-listed-forces-test -cd /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[100%] Built target trajectoryanalysis-test -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[100%] Built target tests -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles 0 -make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -(cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/basic/lib ctest -V) -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/basic/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/basic/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/basic/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/basic/DartConfiguration.tcl -Test project /build/reproducible-path/gromacs-2025.3/build/basic -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -test 1 - Start 1: GmxapiExternalInterfaceTests - -1: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" -1: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests -1: Test timeout computed to be: 600 -1: [==========] Running 9 tests from 1 test suite. -1: [----------] Global test environment set-up. -1: [----------] 9 tests from GmxApiTest -1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to 1123663743 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.863 2.932 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.173 138.980 -1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3326 ms) -1: [ RUN ] GmxApiTest.RunnerBasicMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to 2063071999 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 2.164 1.082 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.468 51.302 -1: [ OK ] GmxApiTest.RunnerBasicMD (1579 ms) -1: [ RUN ] GmxApiTest.RunnerReinitialize -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: -1: Received the remote INT/TERM signal, stopping within 200 steps -1: -1: Setting the LD random seed to -1210081355 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 2.863 1.431 200.0 -1: (ns/day) (hour/ns) -1: Performance: 2.476 9.694 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.728 2.364 200.0 -1: (ns/day) (hour/ns) -1: Performance: 1.499 16.012 -1: [ OK ] GmxApiTest.RunnerReinitialize (4533 ms) -1: [ RUN ] GmxApiTest.RunnerChainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to -1115685956 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.102 2.551 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.198 120.950 -1: trr version: GMX_trn_file (single precision) -1: -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Setting nsteps to 4 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -1: Input file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 2 -1: Runtime for the run 0.00390625 ps -1: Run end step 2 -1: Run end time 0.00390625 ps -1: -1: -1: Output file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 4 -1: Runtime for the run 0.0078125 ps -1: Run end step 4 -1: Run end time 0.0078125 ps -1: -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.714 2.857 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.177 135.440 -1: -1: [ OK ] GmxApiTest.RunnerChainedMD (6227 ms) -1: [ RUN ] GmxApiTest.Status -1: [ OK ] GmxApiTest.Status (0 ms) -1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: Setting the LD random seed to -603979777 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.498 2.749 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.307 78.197 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps -1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -1: -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.377 2.189 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.154 155.649 -1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (5645 ms) -1: [ RUN ] GmxApiTest.SystemConstruction -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Setting the LD random seed to -270599525 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: [ OK ] GmxApiTest.SystemConstruction (243 ms) -1: [ RUN ] GmxApiTest.SaneVersionComparisons -1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) -1: [ RUN ] GmxApiTest.VersionNamed0_1_Features -1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) -1: [----------] 9 tests from GmxApiTest (21555 ms total) -1: -1: [----------] Global test environment tear-down -1: [==========] 9 tests from 1 test suite ran. (21580 ms total) -1: [ PASSED ] 9 tests. - 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 21.60 sec -test 2 - Start 2: GmxapiInternalInterfaceTests - -2: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" -2: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests -2: Test timeout computed to be: 600 -2: [==========] Running 2 tests from 1 test suite. -2: [----------] Global test environment set-up. -2: [----------] 2 tests from GmxApiTest -2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Setting the LD random seed to -20711234 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (322 ms) -2: [ RUN ] GmxApiTest.CreateApiWorkflow -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Setting the LD random seed to -142609153 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: [ OK ] GmxApiTest.CreateApiWorkflow (263 ms) -2: [----------] 2 tests from GmxApiTest (586 ms total) -2: -2: [----------] Global test environment tear-down -2: [==========] 2 tests from 1 test suite ran. (606 ms total) -2: [ PASSED ] 2 tests. - 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.62 sec -test 3 - Start 3: NbLibListedForcesTests - -3: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" -3: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/listed_forces/tests -3: Test timeout computed to be: 600 -3: [==========] Running 44 tests from 22 test suites. -3: [----------] Global test environment set-up. -3: [----------] 8 tests from NBlibTest -3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks -3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) -3: [ RUN ] NBlibTest.BondTypesLessThanWorks -3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) -3: [ RUN ] NBlibTest.CanSplitListedWork -3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) -3: [ RUN ] NBlibTest.ListedForceBuffer -3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) -3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct -3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) -3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes -3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) -3: [ RUN ] NBlibTest.EndToEndListedComparison -3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) -3: [ RUN ] NBlibTest.shiftForcesAreCorrect -3: [ OK ] NBlibTest.shiftForcesAreCorrect (13 ms) -3: [----------] 8 tests from NBlibTest (13 ms total) -3: -3: [----------] 1 test from Kernels -3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute -3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) -3: [----------] 1 test from Kernels (0 ms total) -3: -3: [----------] 1 test from FourCenter -3: [ RUN ] FourCenter.ListedForcesProperDihedralTest -3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) -3: [----------] 1 test from FourCenter (0 ms total) -3: -3: [----------] 7 tests from ThreeCenter -3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest -3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest -3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest -3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest -3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest -3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest -3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest -3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) -3: [----------] 7 tests from ThreeCenter (0 ms total) -3: -3: [----------] 5 tests from TwoCenter -3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest -3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesG96BondTest -3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesCubicBondTest -3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesMorseBondTest -3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesFeneBondTest -3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) -3: [----------] 5 tests from TwoCenter (0 ms total) -3: -3: [----------] 5 tests from ListedExampleData -3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces -3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) -3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies -3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) -3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces -3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) -3: [ RUN ] ListedExampleData.CanReduceForces -3: [ OK ] ListedExampleData.CanReduceForces (0 ms) -3: [ RUN ] ListedExampleData.CanReduceEnergies -3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) -3: [----------] 5 tests from ListedExampleData (0 ms total) -3: -3: [----------] 1 test from LinearChainDataFixture -3: [ RUN ] LinearChainDataFixture.Multithreading -3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) -3: [----------] 1 test from LinearChainDataFixture (0 ms total) -3: -3: [----------] 2 tests from ListedShims -3: [ RUN ] ListedShims.ParameterConversion -3: [ OK ] ListedShims.ParameterConversion (0 ms) -3: [ RUN ] ListedShims.GmxToNblibConversion -3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) -3: [----------] 2 tests from ListedShims (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) -3: -3: [----------] 1 test from ListedTransformations -3: [ RUN ] ListedTransformations.SortInteractionIndices -3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) -3: [----------] 1 test from ListedTransformations (0 ms total) -3: -3: [----------] Global test environment tear-down -3: [==========] 44 tests from 22 test suites ran. (17 ms total) -3: [ PASSED ] 44 tests. - 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.03 sec -test 4 - Start 4: NbLibSamplesTestArgon - -4: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/argon-forces-integration -4: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/samples -4: Test timeout computed to be: 1500 -4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 -4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 -4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 -4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 - 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.01 sec -test 5 - Start 5: NbLibSamplesTestMethaneWater - -5: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/methane-water-integration -5: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/samples -5: Test timeout computed to be: 1500 -5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 -5: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 - 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.01 sec -test 6 - Start 6: NbLibUtilTests - -6: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibUtilTests.xml" -6: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/util/tests -6: Test timeout computed to be: 30 -6: [==========] Running 16 tests from 2 test suites. -6: [----------] Global test environment set-up. -6: [----------] 6 tests from NBlibTest -6: [ RUN ] NBlibTest.isRealValued -6: [ OK ] NBlibTest.isRealValued (0 ms) -6: [ RUN ] NBlibTest.checkNumericValuesHasNan -6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) -6: [ RUN ] NBlibTest.checkNumericValuesHasInf -6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) -6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) -6: [ RUN ] NBlibTest.generateVelocitySize -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.generateVelocitySize (0 ms) -6: [ RUN ] NBlibTest.generateVelocityCheckNumbers -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) -6: [----------] 6 tests from NBlibTest (0 ms total) -6: -6: [----------] 10 tests from NblibTraitsUtils -6: [ RUN ] NblibTraitsUtils.FuseTwo -6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) -6: [ RUN ] NblibTraitsUtils.Fuse -6: [ OK ] NblibTraitsUtils.Fuse (0 ms) -6: [ RUN ] NblibTraitsUtils.Repeat -6: [ OK ] NblibTraitsUtils.Repeat (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 -6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 -6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 -6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 -6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) -6: [ RUN ] NblibTraitsUtils.Contains -6: [ OK ] NblibTraitsUtils.Contains (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated -6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated -6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) -6: [----------] 10 tests from NblibTraitsUtils (0 ms total) -6: -6: [----------] Global test environment tear-down -6: [==========] 16 tests from 2 test suites ran. (0 ms total) -6: [ PASSED ] 16 tests. - 6/92 Test #6: NbLibUtilTests ............................ Passed 0.01 sec -test 7 - Start 7: NbLibSetupTests - -7: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibSetupTests.xml" -7: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests -7: Test timeout computed to be: 600 -7: [==========] Running 57 tests from 3 test suites. -7: [----------] Global test environment set-up. -7: [----------] 41 tests from NBlibTest -7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN -7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) -7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf -7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) -7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN -7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) -7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf -7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) -7: [ RUN ] NBlibTest.CubicBoxWorks -7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) -7: [ RUN ] NBlibTest.BoxEqual -7: [ OK ] NBlibTest.BoxEqual (0 ms) -7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect -7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) -7: [ RUN ] NBlibTest.CanMergeInteractions -7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) -7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed -7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) -7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed -7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) -7: [ RUN ] NBlibTest.PbcHolderWorks -7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) -7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule -7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) -7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames -7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) -7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed -7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) -7: [ RUN ] NBlibTest.AtWorks -7: [ OK ] NBlibTest.AtWorks (0 ms) -7: [ RUN ] NBlibTest.AtThrows -7: [ OK ] NBlibTest.AtThrows (0 ms) -7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass -7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) -7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass -7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) -7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName -7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) -7: [ RUN ] NBlibTest.CanAddInteractions -7: [ OK ] NBlibTest.CanAddInteractions (0 ms) -7: [ RUN ] NBlibTest.CanAddUreyBradley -7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) -7: [ RUN ] NBlibTest.TopologyHasNumParticles -7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) -7: [ RUN ] NBlibTest.TopologyHasCharges -7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) -7: [ RUN ] NBlibTest.TopologyHasMasses -7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) -7: [ RUN ] NBlibTest.TopologyHasParticleTypes -7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) -7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds -7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) -7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType -7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) -7: [ RUN ] NBlibTest.TopologyHasExclusions -7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) -7: [ RUN ] NBlibTest.TopologyHasSequencing -7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) -7: [ RUN ] NBlibTest.TopologyCanAggregateBonds -7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) -7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs -7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) -7: [ RUN ] NBlibTest.TopologySequenceIdThrows -7: No particle O-Atom in residue SOL in molecule SOL found -7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) -7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds -7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) -7: [ RUN ] NBlibTest.TopologyListedInteractions -7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) -7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes -7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) -7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows -7: No particle Iron in residue SOL in molecule SOL found -7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) -7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks -7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) -7: [----------] 41 tests from NBlibTest (1 ms total) -7: -7: [----------] 15 tests from NbnxmSetupTest -7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups -7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) -7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto -7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) -7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount -7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) -7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain -7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) -7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv -7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) -7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks -7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) -7: [ RUN ] NbnxmSetupTest.updateForcerecWorks -7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) -7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup -7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) -7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM -7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) -7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM -7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) -7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU -7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) -7: [----------] 15 tests from NbnxmSetupTest (0 ms total) -7: -7: [----------] 1 test from VirialsTest -7: [ RUN ] VirialsTest.computeVirialTensorWorks -7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) -7: [----------] 1 test from VirialsTest (0 ms total) -7: -7: [----------] Global test environment tear-down -7: [==========] 57 tests from 3 test suites ran. (1 ms total) -7: [ PASSED ] 57 tests. - 7/92 Test #7: NbLibSetupTests ........................... Passed 0.04 sec -test 8 - Start 8: NbLibTprTests - -8: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibTprTests.xml" -8: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests -8: Test timeout computed to be: 30 -8: [==========] Running 4 tests from 1 test suite. -8: [----------] Global test environment set-up. -8: [----------] 4 tests from TprReaderTest -8: [ RUN ] TprReaderTest.SimDBTprIsCreated -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.SimDBTprIsCreated (119 ms) -8: [ RUN ] TprReaderTest.Spc2Reads -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Generating 1-4 interactions: fudge = 0.5 -8: Number of degrees of freedom in T-Coupling group System is 9.00 -8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: NVE simulation: will use the initial temperature of 2573.591 K for -8: determining the Verlet buffer size -8: -8: -8: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: You are using a plain Coulomb cut-off, which might produce artifacts. -8: You might want to consider using PME electrostatics. -8: -8: -8: -8: There were 4 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -8: Generated 3 of the 3 non-bonded parameter combinations -8: -8: Generated 3 of the 3 1-4 parameter combinations -8: -8: Excluding 2 bonded neighbours molecule type 'SOL' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.Spc2Reads (5 ms) -8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (5 ms) -8: [ RUN ] TprReaderTest.FCfromTprDataWorks -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.FCfromTprDataWorks (5 ms) -8: [----------] 4 tests from TprReaderTest (135 ms total) -8: -8: [----------] Global test environment tear-down -8: [==========] 4 tests from 1 test suite ran. (161 ms total) -8: [ PASSED ] 4 tests. - 8/92 Test #8: NbLibTprTests ............................. Passed 0.23 sec -test 9 - Start 9: NbLibIntegrationTests - -9: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" -9: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests -9: Test timeout computed to be: 600 -9: [==========] Running 20 tests from 1 test suite. -9: [----------] Global test environment set-up. -9: [----------] 20 tests from NBlibTest -9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute -9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) -9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect -9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect -9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect -9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect -9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ExpectedNumberOfForces -9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) -9: [ RUN ] NBlibTest.CanIntegrateSystem -9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) -9: [ RUN ] NBlibTest.UpdateChangesForces -9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) -9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect -9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect -9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.CanConstructSimulationState -9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN -9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF -9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN -9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF -9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) -9: [ RUN ] NBlibTest.SimulationStateCanMove -9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) -9: [ RUN ] NBlibTest.SimulationStateCanAssign -9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasBox -9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates -9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities -9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) -9: [----------] 20 tests from NBlibTest (5 ms total) -9: -9: [----------] Global test environment tear-down -9: [==========] 20 tests from 1 test suite ran. (5 ms total) -9: [ PASSED ] 20 tests. - 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.02 sec -test 10 - Start 10: NbLibIntegratorTests - -10: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" -10: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/api/nblib/tests -10: Test timeout computed to be: 600 -10: [==========] Running 1 test from 1 test suite. -10: [----------] Global test environment set-up. -10: [----------] 1 test from NBlibTest -10: [ RUN ] NBlibTest.IntegratorWorks -10: [ OK ] NBlibTest.IntegratorWorks (0 ms) -10: [----------] 1 test from NBlibTest (0 ms total) -10: -10: [----------] Global test environment tear-down -10: [==========] 1 test from 1 test suite ran. (0 ms total) -10: [ PASSED ] 1 test. -10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.01 sec -test 11 - Start 11: TestUtilsUnitTests - -11: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" -11: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/testutils/tests -11: Test timeout computed to be: 30 -11: [==========] Running 75 tests from 7 test suites. -11: [----------] Global test environment set-up. -11: [----------] 10 tests from InteractiveTestHelperTest -11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession -11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (113 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput -11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput -11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput -11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) -11: [----------] 10 tests from InteractiveTestHelperTest (115 ms total) -11: -11: [----------] 10 tests from NameOfTestFromTupleTest -11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple -11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction -11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat -11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter -11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters -11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) -11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) -11: -11: [----------] 3 tests from RefDataFilenameMakerTest -11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction -11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) -11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters -11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) -11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty -11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) -11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) -11: -11: [----------] 37 tests from ReferenceDataTest -11: [ RUN ] ReferenceDataTest.HandlesSimpleData -11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData -11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks -11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesStringBlockData -11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesVectorData -11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceData -11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData -11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesIncorrectData -11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType -11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMissingData -11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedData -11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence -11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound -11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnys -11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree -11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey -11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey -11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue -11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType -11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile -11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings -11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace -11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings -11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock -11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices -11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData -11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds -11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds -11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesReadingValues -11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (109 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) -11: [----------] 37 tests from ReferenceDataTest (114 ms total) -11: -11: [----------] 7 tests from FloatingPointDifferenceTest -11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues -11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues -11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign -11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero -11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences -11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero -11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN -11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) -11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) -11: -11: [----------] 4 tests from FloatingPointToleranceTest -11: [ RUN ] FloatingPointToleranceTest.UlpTolerance -11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) -11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint -11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) -11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp -11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) -11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance -11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) -11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) -11: -11: [----------] 4 tests from XvgTests -11: [ RUN ] XvgTests.CreateFile -11: [ OK ] XvgTests.CreateFile (0 ms) -11: [ RUN ] XvgTests.CheckMissing -11: [ OK ] XvgTests.CheckMissing (0 ms) -11: [ RUN ] XvgTests.CheckExtra -11: [ OK ] XvgTests.CheckExtra (0 ms) -11: [ RUN ] XvgTests.ReadIncorrect -11: [ OK ] XvgTests.ReadIncorrect (0 ms) -11: [----------] 4 tests from XvgTests (0 ms total) -11: -11: [----------] Global test environment tear-down -11: [==========] 75 tests from 7 test suites ran. (230 ms total) -11: [ PASSED ] 75 tests. -11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.24 sec -test 12 - Start 12: TestUtilsMpiUnitTests - -12: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" -12: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/testutils/tests -12: Test timeout computed to be: 30 -12: [==========] Running 1 test from 1 test suite. -12: [----------] Global test environment set-up. -12: [----------] 1 test from MpiSelfTest -12: [ RUN ] MpiSelfTest.Runs -12: [ OK ] MpiSelfTest.Runs (0 ms) -12: [----------] 1 test from MpiSelfTest (0 ms total) -12: -12: [----------] Global test environment tear-down -12: [==========] 1 test from 1 test suite ran. (0 ms total) -12: [ PASSED ] 1 test. -12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.01 sec -test 13 - Start 13: UtilityUnitTests - -13: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/UtilityUnitTests.xml" -13: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/utility/tests -13: Test timeout computed to be: 30 -13: [==========] Running 420 tests from 65 test suites. -13: [----------] Global test environment set-up. -13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.Move -13: [ OK ] AllocatorTest/0.Move (0 ms) -13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/0.Comparison -13: [ OK ] AllocatorTest/0.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/0 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.Move -13: [ OK ] AllocatorTest/1.Move (0 ms) -13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/1.Comparison -13: [ OK ] AllocatorTest/1.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/1 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.Move -13: [ OK ] AllocatorTest/2.Move (0 ms) -13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/2.Comparison -13: [ OK ] AllocatorTest/2.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/2 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.Move -13: [ OK ] AllocatorTest/3.Move (0 ms) -13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/3.Comparison -13: [ OK ] AllocatorTest/3.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/3 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.Move -13: [ OK ] AllocatorTest/4.Move (0 ms) -13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/4.Comparison -13: [ OK ] AllocatorTest/4.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/4 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> -13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.Move -13: [ OK ] AllocatorTest/5.Move (0 ms) -13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/5.Comparison -13: [ OK ] AllocatorTest/5.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/5 (0 ms total) -13: -13: [----------] 1 test from AllocatorUntypedTest -13: [ RUN ] AllocatorUntypedTest.Comparison -13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) -13: [----------] 1 test from AllocatorUntypedTest (0 ms total) -13: -13: [----------] 4 tests from EmptyArrayRefTest -13: [ RUN ] EmptyArrayRefTest.IsEmpty -13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty -13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) -13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr -13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) -13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull -13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) -13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) -13: -13: [----------] 1 test from EmptyConstArrayRefTest -13: [ RUN ] EmptyConstArrayRefTest.IsEmpty -13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) -13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) -13: -13: [----------] 8 tests from BoolType -13: [ RUN ] BoolType.ImplicitConversion -13: [ OK ] BoolType.ImplicitConversion (0 ms) -13: [ RUN ] BoolType.FalseByDefault -13: [ OK ] BoolType.FalseByDefault (0 ms) -13: [ RUN ] BoolType.Assignment -13: [ OK ] BoolType.Assignment (0 ms) -13: [ RUN ] BoolType.Copy -13: [ OK ] BoolType.Copy (0 ms) -13: [ RUN ] BoolType.ArrayRefCanBeCreated -13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) -13: [ RUN ] BoolType.CanBeCastToBool -13: [ OK ] BoolType.CanBeCastToBool (0 ms) -13: [ RUN ] BoolType.HasSizeOfBool -13: [ OK ] BoolType.HasSizeOfBool (0 ms) -13: [ RUN ] BoolType.HasAlignmentOfBool -13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) -13: [----------] 8 tests from BoolType (0 ms total) -13: -13: [----------] 4 tests from ArrayRefFromBoolTypeVector -13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty -13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.Works -13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty -13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks -13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) -13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) -13: -13: [----------] 7 tests from CStringUtilityTest -13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison -13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) -13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength -13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) -13: [ RUN ] CStringUtilityTest.strip_comment -13: [ OK ] CStringUtilityTest.strip_comment (0 ms) -13: [ RUN ] CStringUtilityTest.upstring -13: [ OK ] CStringUtilityTest.upstring (0 ms) -13: [ RUN ] CStringUtilityTest.ltrim -13: [ OK ] CStringUtilityTest.ltrim (0 ms) -13: [ RUN ] CStringUtilityTest.rtrim -13: [ OK ] CStringUtilityTest.rtrim (0 ms) -13: [ RUN ] CStringUtilityTest.trim -13: [ OK ] CStringUtilityTest.trim (0 ms) -13: [----------] 7 tests from CStringUtilityTest (0 ms total) -13: -13: [----------] 2 tests from DefaultInitializationAllocator -13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization -13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) -13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization -13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) -13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) -13: -13: [----------] 4 tests from EnumerationHelpersTest -13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks -13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) -13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks -13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) -13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe -13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) -13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks -13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) -13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) -13: -13: [----------] 1 test from EnumClassSuitsEnumerationArray -13: [ RUN ] EnumClassSuitsEnumerationArray.Works -13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) -13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) -13: -13: [----------] 18 tests from FixedCapacityVectorTest -13: [ RUN ] FixedCapacityVectorTest.IsEmpty -13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks -13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.PushWorks -13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.PopWorks -13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ResizeWorks -13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ClearWorks -13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks -13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.AtThrows -13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) -13: [ RUN ] FixedCapacityVectorTest.IteratorWorks -13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks -13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks -13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks -13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks -13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.DataWorks -13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork -13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) -13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) -13: -13: [----------] 5 tests from InMemorySerializerTest -13: [ RUN ] InMemorySerializerTest.Roundtrip -13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) -13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap -13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap -13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap -13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.SizeIsCorrect -13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) -13: [----------] 5 tests from InMemorySerializerTest (0 ms total) -13: -13: [----------] 4 tests from KeyValueTreeSerializerTest -13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree -13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject -13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays -13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects -13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) -13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) -13: -13: [----------] 7 tests from TreeValueTransformTest -13: [ RUN ] TreeValueTransformTest.SimpleTransforms -13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) -13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive -13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) -13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject -13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) -13: [ RUN ] TreeValueTransformTest.ObjectFromString -13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) -13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings -13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) -13: [ RUN ] TreeValueTransformTest.ScopedTransformRules -13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) -13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue -13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) -13: [----------] 7 tests from TreeValueTransformTest (0 ms total) -13: -13: [----------] 1 test from TreeValueTransformErrorTest -13: [ RUN ] TreeValueTransformErrorTest.ConversionError -13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) -13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) -13: -13: [----------] 9 tests from ListOfLists -13: [ RUN ] ListOfLists.EmptyListOfListsWorks -13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) -13: [ RUN ] ListOfLists.AppendWorks -13: [ OK ] ListOfLists.AppendWorks (0 ms) -13: [ RUN ] ListOfLists.EmptyListWorks -13: [ OK ] ListOfLists.EmptyListWorks (0 ms) -13: [ RUN ] ListOfLists.AppendAccessWorks -13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) -13: [ RUN ] ListOfLists.ClearWorks -13: [ OK ] ListOfLists.ClearWorks (0 ms) -13: [ RUN ] ListOfLists.OutOfRangeAccessThrows -13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) -13: [ RUN ] ListOfLists.FrontAndBackWork -13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) -13: [ RUN ] ListOfLists.ExtractsAndRestores -13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) -13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset -13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) -13: [----------] 9 tests from ListOfLists (0 ms total) -13: -13: [----------] 7 tests from LoggerTest -13: [ RUN ] LoggerTest.EmptyLoggerWorks -13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) -13: [ RUN ] LoggerTest.LogsToStream -13: [ OK ] LoggerTest.LogsToStream (0 ms) -13: [ RUN ] LoggerTest.LogsToFile -13: [ OK ] LoggerTest.LogsToFile (0 ms) -13: [ RUN ] LoggerTest.LevelFilteringWorks -13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) -13: [ RUN ] LoggerTest.LogsToMultipleStreams -13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) -13: [ RUN ] LoggerTest.LogsToMultipleFiles -13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) -13: [ RUN ] LoggerTest.LogsToStreamAndFile -13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) -13: [----------] 7 tests from LoggerTest (1 ms total) -13: -13: [----------] 7 tests from MessageStringCollectorTest -13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext -13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext -13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages -13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally -13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally -13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct -13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanMoveAssign -13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) -13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) -13: -13: [----------] 1 test from PathTest -13: [ RUN ] PathTest.StripSourcePrefixWorks -13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) -13: [----------] 1 test from PathTest (0 ms total) -13: -13: [----------] 2 tests from PhysicalNodeCommunicatorTest -13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -13: -13: [----------] 5 tests from Range -13: [ RUN ] Range.EmptyRangeWorks -13: [ OK ] Range.EmptyRangeWorks (0 ms) -13: [ RUN ] Range.NonEmptyRangeWorks -13: [ OK ] Range.NonEmptyRangeWorks (0 ms) -13: [ RUN ] Range.BeginEnd -13: [ OK ] Range.BeginEnd (0 ms) -13: [ RUN ] Range.IsInRangeWorks -13: [ OK ] Range.IsInRangeWorks (0 ms) -13: [ RUN ] Range.IteratorWorks -13: [ OK ] Range.IteratorWorks (0 ms) -13: [----------] 5 tests from Range (0 ms total) -13: -13: [----------] 3 tests from ScopeGuardTest -13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit -13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) -13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers -13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) -13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions -13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) -13: [----------] 3 tests from ScopeGuardTest (0 ms total) -13: -13: [----------] 7 tests from StringConvert -13: [ RUN ] StringConvert.NoResultFromEptyString -13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) -13: [ RUN ] StringConvert.ThreeFloatsSuccessfully -13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) -13: [ RUN ] StringConvert.OneIntSucessfully -13: [ OK ] StringConvert.OneIntSucessfully (0 ms) -13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows -13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) -13: [ RUN ] StringConvert.ThrowsWhenWrongSize -13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) -13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows -13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) -13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay -13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) -13: [----------] 7 tests from StringConvert (0 ms total) -13: -13: [----------] 7 tests from StringToEnumValueConverterTest -13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks -13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) -13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) -13: -13: [----------] 9 tests from StringUtilityTest -13: [ RUN ] StringUtilityTest.StartsWith -13: [ OK ] StringUtilityTest.StartsWith (0 ms) -13: [ RUN ] StringUtilityTest.EndsWith -13: [ OK ] StringUtilityTest.EndsWith (0 ms) -13: [ RUN ] StringUtilityTest.StripSuffixIfPresent -13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) -13: [ RUN ] StringUtilityTest.StripString -13: [ OK ] StringUtilityTest.StripString (0 ms) -13: [ RUN ] StringUtilityTest.SplitString -13: [ OK ] StringUtilityTest.SplitString (0 ms) -13: [ RUN ] StringUtilityTest.SplitDelimitedString -13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) -13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString -13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) -13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive -13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) -13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength -13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) -13: [----------] 9 tests from StringUtilityTest (0 ms total) -13: -13: [----------] 2 tests from FormatStringTest -13: [ RUN ] FormatStringTest.HandlesBasicFormatting -13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) -13: [ RUN ] FormatStringTest.HandlesLongStrings -13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) -13: [----------] 2 tests from FormatStringTest (0 ms total) -13: -13: [----------] 1 test from StringFormatterTest -13: [ RUN ] StringFormatterTest.HandlesBasicFormatting -13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) -13: [----------] 1 test from StringFormatterTest (0 ms total) -13: -13: [----------] 1 test from formatAndJoinTest -13: [ RUN ] formatAndJoinTest.Works -13: [ OK ] formatAndJoinTest.Works (0 ms) -13: [----------] 1 test from formatAndJoinTest (0 ms total) -13: -13: [----------] 1 test from JoinStringsTest -13: [ RUN ] JoinStringsTest.Works -13: [ OK ] JoinStringsTest.Works (0 ms) -13: [----------] 1 test from JoinStringsTest (0 ms total) -13: -13: [----------] 6 tests from ReplaceAllTest -13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings -13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesNoMatches -13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds -13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches -13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries -13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches -13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) -13: [----------] 6 tests from ReplaceAllTest (0 ms total) -13: -13: [----------] 10 tests from TextLineWrapperTest -13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings -13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace -13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines -13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectly -13: [ OK ] TextLineWrapperTest.WrapsCorrectly (103 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks -13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesIndent -13: [ OK ] TextLineWrapperTest.HandlesIndent (72 ms) -13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines -13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent -13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter -13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace -13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) -13: [----------] 10 tests from TextLineWrapperTest (176 ms total) -13: -13: [----------] 1 test from CompileTimeStringJoin -13: [ RUN ] CompileTimeStringJoin.Works -13: [ OK ] CompileTimeStringJoin.Works (0 ms) -13: [----------] 1 test from CompileTimeStringJoin (0 ms total) -13: -13: [----------] 3 tests from TemplateMPTest -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) -13: [----------] 3 tests from TemplateMPTest (0 ms total) -13: -13: [----------] 6 tests from TextWriterTest -13: [ RUN ] TextWriterTest.WritesLines -13: [ OK ] TextWriterTest.WritesLines (0 ms) -13: [ RUN ] TextWriterTest.WritesLinesInParts -13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) -13: [ RUN ] TextWriterTest.WritesWrappedLines -13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) -13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper -13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) -13: [ RUN ] TextWriterTest.TracksNewlines -13: [ OK ] TextWriterTest.TracksNewlines (0 ms) -13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace -13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) -13: [----------] 6 tests from TextWriterTest (0 ms total) -13: -13: [----------] 1 test from TypeTraitsTest -13: [ RUN ] TypeTraitsTest.IsIntegralConstant -13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) -13: [----------] 1 test from TypeTraitsTest (0 ms total) -13: -13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) -13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) -13: -13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) -13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) -13: -13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) -13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) -13: -13: [----------] 11 tests from WithInputPaths/PathSearchTest -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) -13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) -13: -13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) -13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) -13: -13: [----------] Global test environment tear-down -13: [==========] 420 tests from 65 test suites ran. (184 ms total) -13: [ PASSED ] 420 tests. -13: -13: YOU HAVE 1 DISABLED TEST -13: -13/92 Test #13: UtilityUnitTests .......................... Passed 0.20 sec -test 14 - Start 14: UtilityMpiUnitTests - -14: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" -14: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/utility/tests -14: Test timeout computed to be: 30 -14: [==========] Running 2 tests from 1 test suite. -14: [----------] Global test environment set-up. -14: [----------] 2 tests from PhysicalNodeCommunicatorTest -14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -14: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -14: -14: [----------] Global test environment tear-down -14: [==========] 2 tests from 1 test suite ran. (0 ms total) -14: [ PASSED ] 2 tests. -14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.01 sec -test 15 - Start 15: GmxlibTests - -15: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxlibTests.xml" -15: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxlib/nonbonded/tests -15: Test timeout computed to be: 30 -15: [==========] Running 78 tests from 2 test suites. -15: [----------] Global test environment set-up. -15: [----------] 72 tests from NBInteraction/NonbondedFepTest -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) -15: [----------] 72 tests from NBInteraction/NonbondedFepTest (9 ms total) -15: -15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) -15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) -15: -15: [----------] Global test environment tear-down -15: [==========] 78 tests from 2 test suites ran. (10 ms total) -15: [ PASSED ] 78 tests. -15/92 Test #15: GmxlibTests ............................... Passed 0.03 sec -test 16 - Start 16: MdlibUnitTest - -16: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdlibUnitTest.xml" -16: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests -16: Test timeout computed to be: 30 -16: [==========] Running 1032 tests from 27 test suites. -16: [----------] Global test environment set-up. -16: [----------] 3 tests from EffectiveAtomDensity -16: [ RUN ] EffectiveAtomDensity.VolumeIndependence -16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) -16: [ RUN ] EffectiveAtomDensity.WeightingWorks -16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) -16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell -16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) -16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) -16: -16: [----------] 2 tests from AtomNonbondedAndKineticProperties -16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate -16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) -16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork -16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) -16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) -16: -16: [----------] 1 test from VerletBufferConstraintTest -16: [ RUN ] VerletBufferConstraintTest.EqualMasses -16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) -16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) -16: -16: [----------] 1 test from VerletBufferSize -16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent -16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) -16: [----------] 1 test from VerletBufferSize (0 ms total) -16: -16: [----------] 6 tests from CalcvirTest -16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox -16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew -16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) -16: [----------] 6 tests from CalcvirTest (0 ms total) -16: -16: [----------] 2 tests from PrEbinTest -16: [ RUN ] PrEbinTest.HandlesAverages -16: [ OK ] PrEbinTest.HandlesAverages (0 ms) -16: [ RUN ] PrEbinTest.HandlesEmptyAverages -16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) -16: [----------] 2 tests from PrEbinTest (0 ms total) -16: -16: [----------] 3 tests from EnergyDriftTracker -16: [ RUN ] EnergyDriftTracker.emptyWorks -16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) -16: [ RUN ] EnergyDriftTracker.onePointWorks -16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) -16: [ RUN ] EnergyDriftTracker.manyPointsWorks -16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) -16: [----------] 3 tests from EnergyDriftTracker (0 ms total) -16: -16: [----------] 4 tests from ShakeTest -16: [ RUN ] ShakeTest.ConstrainsOneBond -16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) -16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds -16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) -16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom -16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) -16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms -16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) -16: [----------] 4 tests from ShakeTest (0 ms total) -16: -16: [----------] 1 test from NullSignalTest -16: [ RUN ] NullSignalTest.NullSignallerWorks -16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) -16: [----------] 1 test from NullSignalTest (0 ms total) -16: -16: [----------] 7 tests from SignalTest -16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace -16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace -16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace -16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace -16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) -16: [----------] 7 tests from SignalTest (0 ms total) -16: -16: [----------] 13 tests from UpdateGroupsTest -16: [ RUN ] UpdateGroupsTest.WithEthaneUA -16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) -16: [ RUN ] UpdateGroupsTest.WithMethane -16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) -16: [ RUN ] UpdateGroupsTest.WithEthane -16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) -16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane -16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) -16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups -16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite -16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterFourSite -16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) -16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle -16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle -16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) -16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle -16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) -16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes -16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) -16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid -16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) -16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful -16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) -16: [----------] 13 tests from UpdateGroupsTest (0 ms total) -16: -16: [----------] 1 test from UpdateGroupsCog -16: [ RUN ] UpdateGroupsCog.ComputesCogs -16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) -16: [----------] 1 test from UpdateGroupsCog (0 ms total) -16: -16: [----------] 2 tests from WholeMoleculeTransform -16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole -16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) -16: [ RUN ] WholeMoleculeTransform.HandlesReordering -16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) -16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) -16: -16: [----------] 28 tests from WithParameters/ConstraintsTest -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (147 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) -16: [----------] 28 tests from WithParameters/ConstraintsTest (157 ms total) -16: -16: [----------] 11 tests from WithParameters/EnergyOutputTest -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (14 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 -16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file -16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (4 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (1 ms) -16: [----------] 11 tests from WithParameters/EnergyOutputTest (28 ms total) -16: -16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) -16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) -16: -16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) -16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) -16: -16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) -16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) -16: -16: [----------] 17 tests from WithParameters/LangevinTest -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) -16: [----------] 17 tests from WithParameters/LangevinTest (2 ms total) -16: -16: [----------] 16 tests from WithParameters/LeapFrogTest -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) -16: [----------] 16 tests from WithParameters/LeapFrogTest (12 ms total) -16: -16: [----------] 140 tests from Cubic/ParrRahmTest -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Cubic/ParrRahmTest (9 ms total) -16: -16: [----------] 140 tests from Rectilinear/ParrRahmTest -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Rectilinear/ParrRahmTest (8 ms total) -16: -16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (8 ms total) -16: -16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (9 ms total) -16: -16: [----------] 140 tests from TruncOct/ParrRahmTest -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from TruncOct/ParrRahmTest (9 ms total) -16: -16: [----------] 140 tests from Other/ParrRahmTest -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Other/ParrRahmTest (8 ms total) -16: -16: [----------] 13 tests from WithParameters/SettleTest -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) -16: [----------] 13 tests from WithParameters/SettleTest (4 ms total) -16: -16: [----------] Global test environment tear-down -16: [==========] 1032 tests from 27 test suites ran. (263 ms total) -16: [ PASSED ] 1032 tests. -16/92 Test #16: MdlibUnitTest ............................. Passed 0.43 sec -test 17 - Start 17: AwhTest - -17: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/AwhTest.xml" -17: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/awh/tests -17: Test timeout computed to be: 30 -17: [==========] Running 27 tests from 10 test suites. -17: [----------] Global test environment set-up. -17: [----------] 3 tests from SerializationTest -17: [ RUN ] SerializationTest.CanSerializeDimParams -17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) -17: [ RUN ] SerializationTest.CanSerializeBiasParams -17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) -17: [ RUN ] SerializationTest.CanSerializeAwhParams -17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) -17: [----------] 3 tests from SerializationTest (0 ms total) -17: -17: [----------] 1 test from BiasTest -17: [ RUN ] BiasTest.DetectsCovering -17: [ OK ] BiasTest.DetectsCovering (0 ms) -17: [----------] 1 test from BiasTest (0 ms total) -17: -17: [----------] 1 test from biasGridTest -17: [ RUN ] biasGridTest.neighborhood -17: [ OK ] biasGridTest.neighborhood (1 ms) -17: [----------] 1 test from biasGridTest (1 ms total) -17: -17: [----------] 2 tests from BiasSharingTest -17: [ RUN ] BiasSharingTest.SharingWorks -17: [ OK ] BiasSharingTest.SharingWorks (0 ms) -17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks -17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (1 ms) -17: [----------] 2 tests from BiasSharingTest (2 ms total) -17: -17: [----------] 2 tests from BiasFepLambdaStateTest -17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering -17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (2 ms) -17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy -17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) -17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) -17: -17: [----------] 8 tests from WithParameters/BiasTest -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) -17: [----------] 8 tests from WithParameters/BiasTest (3 ms total) -17: -17: [----------] 2 tests from WithParameters/BiasStateTest -17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 -17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) -17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 -17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) -17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) -17: -17: [----------] 1 test from WithParameters/UserInputTest -17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 -17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) -17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) -17: -17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (4 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) -17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (16 ms total) -17: -17: [----------] 3 tests from WithParameters/FrictionMetricTest -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) -17: [----------] 3 tests from WithParameters/FrictionMetricTest (13 ms total) -17: -17: [----------] Global test environment tear-down -17: [==========] 27 tests from 10 test suites ran. (42 ms total) -17: [ PASSED ] 27 tests. -17/92 Test #17: AwhTest ................................... Passed 0.06 sec -test 18 - Start 18: DensityFittingAppliedForcesUnitTest - -18: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" -18: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/densityfitting/tests -18: Test timeout computed to be: 30 -18: [==========] Running 18 tests from 4 test suites. -18: [----------] Global test environment set-up. -18: [----------] 2 tests from DensityFittingTest -18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows -18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) -18: [ RUN ] DensityFittingTest.SingleAtom -18: [ OK ] DensityFittingTest.SingleAtom (0 ms) -18: [----------] 2 tests from DensityFittingTest (0 ms total) -18: -18: [----------] 7 tests from DensityFittingAmplitudeLookupTest -18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity -18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge -18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses -18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign -18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct -18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign -18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct -18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) -18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) -18: -18: [----------] 1 test from DensityFittingForceProviderState -18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving -18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) -18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) -18: -18: [----------] 8 tests from DensityFittingOptionsTest -18: [ RUN ] DensityFittingOptionsTest.DefaultParameters -18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive -18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive -18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive -18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup -18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt -18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) -18: [ RUN ] DensityFittingOptionsTest.KvtToInternal -18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) -18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent -18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) -18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) -18: -18: [----------] Global test environment tear-down -18: [==========] 18 tests from 4 test suites ran. (1 ms total) -18: [ PASSED ] 18 tests. -18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.01 sec -test 19 - Start 19: QMMMAppliedForcesUnitTest - -19: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" -19: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests -19: Test timeout computed to be: 30 -19: [==========] Running 21 tests from 5 test suites. -19: [----------] Global test environment set-up. -19: [----------] 3 tests from QMMMInputGeneratorTest -19: [ RUN ] QMMMInputGeneratorTest.CanConstruct -19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) -19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink -19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) -19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink -19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) -19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) -19: -19: [----------] 7 tests from QMMMTopologyPreprocessorTest -19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct -19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to 2145304511 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to -545804931 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (93 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to -286156163 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (375 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 63.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: NVE simulation: will use the initial temperature of 129.093 K for -19: determining the Verlet buffer size -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to -12583617 -19: -19: Generated 2145 of the 2145 non-bonded parameter combinations -19: -19: Generated 2145 of the 2145 1-4 parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -19: Analysing residue names: -19: There are: 3 Protein residues -19: Analysing Protein... -19: -19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -19: -19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -19: -19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -19: -19: Note that mdrun will redetermine rlist based on the actual pair-list setup -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (162 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: -19: NOTE 2 [file unknown]: -19: You are using constraints on all bonds, whereas the forcefield has been -19: parametrized only with constraints involving hydrogen atoms. We suggest -19: using constraints = h-bonds instead, this will also improve performance. -19: -19: -19: NOTE 3 [file unknown]: -19: For energy conservation with LINCS, lincs_iter should be 2 or larger. -19: -19: -19: Number of degrees of freedom in T-Coupling group rest is 42.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: NVE simulation: will use the initial temperature of 193.640 K for -19: determining the Verlet buffer size -19: -19: -19: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 5 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to -1078460418 -19: -19: Generated 2145 of the 2145 non-bonded parameter combinations -19: -19: Generated 2145 of the 2145 1-4 parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -19: -19: turning all bonds into constraints... -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -19: Analysing residue names: -19: There are: 3 Protein residues -19: Analysing Protein... -19: -19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -19: -19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -19: -19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -19: -19: Note that mdrun will redetermine rlist based on the actual pair-list setup -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (373 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Number of degrees of freedom in T-Coupling group rest is 45.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -19: Setting the LD random seed to -411370757 -19: -19: Generated 3 of the 6 non-bonded parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'VSTEST' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -19: -19: Cleaning up constraints and constant bonded interactions with virtual sites -19: Analysing residue names: -19: There are: 1 Other residues -19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (135 ms) -19: [----------] 7 tests from QMMMTopologyPreprocessorTest (1143 ms total) -19: -19: [----------] 9 tests from QMMMOptionsTest -19: [ RUN ] QMMMOptionsTest.DefaultParameters -19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) -19: [ RUN ] QMMMOptionsTest.OptionSetsActive -19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) -19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive -19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive -19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) -19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack -19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) -19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing -19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) -19: [----------] 9 tests from QMMMOptionsTest (1 ms total) -19: -19: [----------] 1 test from QMMMForceProviderTest -19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot -19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) -19: [----------] 1 test from QMMMForceProviderTest (0 ms total) -19: -19: [----------] 1 test from QMMMTest -19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows -19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) -19: [----------] 1 test from QMMMTest (0 ms total) -19: -19: [----------] Global test environment tear-down -19: [==========] 21 tests from 5 test suites ran. (1146 ms total) -19: [ PASSED ] 21 tests. -19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 1.16 sec -test 20 - Start 20: ColvarsAppliedForcesUnitTest - -20: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" -20: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests -20: Test timeout computed to be: 30 -20: [==========] Running 16 tests from 4 test suites. -20: [----------] Global test environment set-up. -20: [----------] 1 test from ColvarsTest -20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows -20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) -20: [----------] 1 test from ColvarsTest (0 ms total) -20: -20: [----------] 6 tests from ColvarsOptionsTest -20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive -20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive -20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive -20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OptionSetsActive -20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to 1878694310 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (4 ms) -20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename -20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) -20: [----------] 6 tests from ColvarsOptionsTest (5 ms total) -20: -20: [----------] 4 tests from ColvarsPreProcessorTest -20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to -806027266 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (67 ms) -20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to 2128379609 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (239 ms) -20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to -1146225025 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (516 ms) -20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to -855656481 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (43 ms) -20: [----------] 4 tests from ColvarsPreProcessorTest (867 ms total) -20: -20: [----------] 5 tests from ColvarsForceProviderTest -20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot -20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) -20: [ RUN ] ColvarsForceProviderTest.SimpleInputs -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to 2109470142 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.SimpleInputs (173 ms) -20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to 1071389927 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (235 ms) -20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to -613050449 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (184 ms) -20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 66.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: NVE simulation: will use the initial temperature of 300.368 K for -20: determining the Verlet buffer size -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -20: Setting the LD random seed to 1576525683 -20: -20: Generated 2211 of the 2211 non-bonded parameter combinations -20: -20: Generated 2211 of the 2211 1-4 parameter combinations -20: -20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -20: Analysing residue names: -20: There are: 2 Protein residues -20: Analysing Protein... -20: -20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -20: -20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -20: -20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -20: -20: Note that mdrun will redetermine rlist based on the actual pair-list setup -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (22 ms) -20: [----------] 5 tests from ColvarsForceProviderTest (616 ms total) -20: -20: [----------] Global test environment tear-down -20: [==========] 16 tests from 4 test suites ran. (1489 ms total) -20: [ PASSED ] 16 tests. -20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 1.50 sec -test 21 - Start 21: PlumedAppliedForcesUnitTests - -21: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" -21: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests -21: Test timeout computed to be: 30 -21: [==========] Running 8 tests from 1 test suite. -21: [----------] Global test environment set-up. -21: [----------] 8 tests from PlumedOptionsTest -21: [ RUN ] PlumedOptionsTest.defaultConstructor -21: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) -21: [ RUN ] PlumedOptionsTest.setTimeStep -21: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) -21: [ RUN ] PlumedOptionsTest.setStartingBehavior -21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) -21: [ RUN ] PlumedOptionsTest.setPlumedFile -21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) -21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet -21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) -21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data -21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) -21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant -21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) -21: [ RUN ] PlumedOptionsTest.setTopology -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 21.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: -21: NOTE 2 [file angles1.top, line 72]: -21: In moleculetype 'butane' 4 atoms are not bound by a potential or -21: constraint to any other atom in the same moleculetype. Although -21: technically this might not cause issues in a simulation, this often means -21: that the user forgot to add a bond/potential/constraint or put multiple -21: molecules in the same moleculetype definition by mistake. Run with -v to -21: get information for each atom. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -21: NVE simulation: will use the initial temperature of 238.919 K for -21: determining the Verlet buffer size -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 17493.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -21: NVE simulation: will use the initial temperature of 67.983 K for -21: determining the Verlet buffer size -21: -21: -21: There were 2 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: There were 2 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 18.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: NVE simulation: will use the initial temperature of 135.187 K for -21: determining the Verlet buffer size -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to 2147455455 -21: -21: Generated 10 of the 10 non-bonded parameter combinations -21: -21: Generated 10 of the 10 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Water residues -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -167920643 -21: -21: Generated 3 of the 3 non-bonded parameter combinations -21: -21: Excluding 3 bonded neighbours molecule type 'butane' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/angles1.gro' -21: Analysing residue names: -21: There are: 1 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -1075978243 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'Argon' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon5832.gro' -21: Analysing residue names: -21: There are: 5832 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -17826051 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonA' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonB' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonC' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonD' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -1271927076 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'Dipole' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -21: Analysing residue names: -21: There are: 2 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -1610612993 -21: -21: Generated 331705 of the 331705 non-bonded parameter combinations -21: -21: Generated 331705 of the 331705 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Excluding 3 bonded neighbours molecule type 'methane' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -21: Analysing residue names: -21: There are: 1 Water residues -21: There are: 1 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] PlumedOptionsTest.setTopology (1015 ms) -21: [----------] 8 tests from PlumedOptionsTest (1017 ms total) -21: -21: [----------] Global test environment tear-down -21: [==========] 8 tests from 1 test suite ran. (1017 ms total) -21: [ PASSED ] 8 tests. -21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 1.03 sec -test 22 - Start 22: PlumedMDTests - -22: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/PlumedMDTests.xml" -22: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/plumed/tests -22: Test timeout computed to be: 600 -22: [==========] Running 2 tests from 1 test suite. -22: [----------] Global test environment set-up. -22: [----------] 2 tests from SimplePlumedMD/PlumedRun -22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 -22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) -22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) -22: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) -22: -22: [----------] Global test environment tear-down -22: [==========] 2 tests from 1 test suite ran. (29 ms total) -22: [ PASSED ] 0 tests. -22: [ SKIPPED ] 2 tests, listed below: -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -22/92 Test #22: PlumedMDTests ............................. Passed 0.04 sec -test 23 - Start 23: NNPotAppliedForcesUnitTest - -23: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" -23: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests -23: Test timeout computed to be: 30 -23: [==========] Running 12 tests from 4 test suites. -23: [----------] Global test environment set-up. -23: [----------] 1 test from NNPotTest -23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows -23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) -23: [----------] 1 test from NNPotTest (0 ms total) -23: -23: [----------] 5 tests from NNPotOptionsTest -23: [ RUN ] NNPotOptionsTest.DefaultParameters -23: [ OK ] NNPotOptionsTest.DefaultParameters (88 ms) -23: [ RUN ] NNPotOptionsTest.OptionSetsActive -23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) -23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive -23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive -23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) -23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack -23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) -23: [----------] 5 tests from NNPotOptionsTest (88 ms total) -23: -23: [----------] 5 tests from NNPotTopologyPreprocessorTest -23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct -23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 21.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Setting the LD random seed to -1610762431 -23: -23: Generated 10 of the 10 non-bonded parameter combinations -23: -23: Generated 10 of the 10 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Water residues -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (40 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 21.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Setting the LD random seed to -5251081 -23: -23: Generated 10 of the 10 non-bonded parameter combinations -23: -23: Generated 10 of the 10 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Water residues -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (176 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 63.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: NVE simulation: will use the initial temperature of 129.093 K for -23: determining the Verlet buffer size -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Setting the LD random seed to -88277586 -23: -23: Generated 2145 of the 2145 non-bonded parameter combinations -23: -23: Generated 2145 of the 2145 1-4 parameter combinations -23: -23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -23: Analysing residue names: -23: There are: 3 Protein residues -23: Analysing Protein... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (188 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: -23: NOTE 2 [file unknown]: -23: You are using constraints on all bonds, whereas the forcefield has been -23: parametrized only with constraints involving hydrogen atoms. We suggest -23: using constraints = h-bonds instead, this will also improve performance. -23: -23: -23: NOTE 3 [file unknown]: -23: For energy conservation with LINCS, lincs_iter should be 2 or larger. -23: -23: -23: Number of degrees of freedom in T-Coupling group rest is 42.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: NVE simulation: will use the initial temperature of 193.640 K for -23: determining the Verlet buffer size -23: -23: -23: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 5 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Setting the LD random seed to -1723875396 -23: -23: Generated 2145 of the 2145 non-bonded parameter combinations -23: -23: Generated 2145 of the 2145 1-4 parameter combinations -23: -23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -23: -23: turning all bonds into constraints... -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -23: Analysing residue names: -23: There are: 3 Protein residues -23: Analysing Protein... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (105 ms) -23: [----------] 5 tests from NNPotTopologyPreprocessorTest (512 ms total) -23: -23: [----------] 1 test from NNPotForceProviderTest -23: [ RUN ] NNPotForceProviderTest.CanConstruct -23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) -23: [----------] 1 test from NNPotForceProviderTest (0 ms total) -23: -23: [----------] Global test environment tear-down -23: [==========] 12 tests from 4 test suites ran. (601 ms total) -23: [ PASSED ] 12 tests. -23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.64 sec -test 24 - Start 24: AppliedForcesUnitTest - -24: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" -24: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/applied_forces/tests -24: Test timeout computed to be: 30 -24: [==========] Running 3 tests from 1 test suite. -24: [----------] Global test environment set-up. -24: [----------] 3 tests from ElectricFieldTest -24: [ RUN ] ElectricFieldTest.Static -24: [ OK ] ElectricFieldTest.Static (0 ms) -24: [ RUN ] ElectricFieldTest.Oscillating -24: [ OK ] ElectricFieldTest.Oscillating (0 ms) -24: [ RUN ] ElectricFieldTest.Pulsed -24: [ OK ] ElectricFieldTest.Pulsed (0 ms) -24: [----------] 3 tests from ElectricFieldTest (0 ms total) -24: -24: [----------] Global test environment tear-down -24: [==========] 3 tests from 1 test suite ran. (0 ms total) -24: [ PASSED ] 3 tests. -24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.01 sec -test 25 - Start 25: ListedForcesTest - -25: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/ListedForcesTest.xml" -25: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/listed_forces/tests -25: Test timeout computed to be: 30 -25: [==========] Running 132 tests from 9 test suites. -25: [----------] Global test environment set-up. -25: [----------] 24 tests from Bond/ListedForcesTest -25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 -25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (65 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 -25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 -25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 -25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 -25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 -25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 -25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 -25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 -25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 -25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 -25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 -25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 -25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 -25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 -25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 -25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 -25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 -25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 -25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 -25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 -25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 -25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 -25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 -25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) -25: [----------] 24 tests from Bond/ListedForcesTest (70 ms total) -25: -25: [----------] 33 tests from Angle/ListedForcesTest -25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 -25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 -25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 -25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 -25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 -25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 -25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 -25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 -25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 -25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 -25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 -25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 -25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 -25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 -25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 -25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 -25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 -25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 -25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 -25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 -25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 -25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 -25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 -25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 -25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 -25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 -25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 -25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 -25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 -25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 -25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 -25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 -25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 -25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) -25: [----------] 33 tests from Angle/ListedForcesTest (7 ms total) -25: -25: [----------] 18 tests from Dihedral/ListedForcesTest -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) -25: [----------] 18 tests from Dihedral/ListedForcesTest (3 ms total) -25: -25: [----------] 12 tests from Polarize/ListedForcesTest -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) -25: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) -25: -25: [----------] 18 tests from Restraints/ListedForcesTest -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) -25: [----------] 18 tests from Restraints/ListedForcesTest (4 ms total) -25: -25: [----------] 3 tests from BondZeroLength/ListedForcesTest -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) -25: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) -25: -25: [----------] 3 tests from AngleZero/ListedForcesTest -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) -25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) -25: -25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) -25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (2 ms total) -25: -25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) -25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) -25: -25: [----------] Global test environment tear-down -25: [==========] 132 tests from 9 test suites ran. (92 ms total) -25: [ PASSED ] 132 tests. -25/92 Test #25: ListedForcesTest .......................... Passed 0.13 sec -test 26 - Start 26: NbnxmTests - -26: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbnxmTests.xml" -26: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/nbnxm/tests -26: Test timeout computed to be: 30 -26: [==========] Running 383 tests from 4 test suites. -26: [----------] Global test environment set-up. -26: [----------] 18 tests from KernelSetupTest -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF -26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut -26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable -26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin -26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald -26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin -26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom -26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone -26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows -26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) -26: [----------] 18 tests from KernelSetupTest (0 ms total) -26: -26: [----------] 2 tests from SimdEnergyAccumulatorTest -26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM -26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) -26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM -26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) -26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) -26: -26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) -26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) -26: -26: [----------] 360 tests from Combinations/NbnxmKernelTest -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (93 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (10 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (31 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (75 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (93 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [----------] 360 tests from Combinations/NbnxmKernelTest (676 ms total) -26: -26: [----------] Global test environment tear-down -26: [==========] 383 tests from 4 test suites ran. (677 ms total) -26: [ PASSED ] 185 tests. -26: [ SKIPPED ] 198 tests, listed below: -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26/92 Test #26: NbnxmTests ................................ Passed 0.70 sec -test 27 - Start 27: NbnxmGpuTests - -27: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/NbnxmGpuTests.xml" -27: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/nbnxm/tests -27: Test timeout computed to be: 30 -27: [==========] Running 0 tests from 0 test suites. -27: [==========] 0 tests from 0 test suites ran. (0 ms total) -27: [ PASSED ] 0 tests. -27/92 Test #27: NbnxmGpuTests ............................. Passed 0.05 sec -test 28 - Start 28: CommandLineUnitTests - -28: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/CommandLineUnitTests.xml" -28: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests -28: Test timeout computed to be: 30 -28: [==========] Running 60 tests from 7 test suites. -28: [----------] Global test environment set-up. -28: [----------] 3 tests from CommandLineHelpModuleTest -28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp -28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) -28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic -28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) -28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp -28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (51 ms) -28: [----------] 3 tests from CommandLineHelpModuleTest (52 ms total) -28: -28: [----------] 7 tests from CommandLineHelpWriterTest -28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes -28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables -28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions -28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions -28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups -28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText -28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues -28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) -28: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) -28: -28: [----------] 6 tests from CommandLineModuleManagerTest -28: [ RUN ] CommandLineModuleManagerTest.RunsModule -28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames -28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) -28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) -28: -28: [----------] 13 tests from CommandLineParserTest -28: [ RUN ] CommandLineParserTest.HandlesSingleValues -28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument -28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument -28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) -28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument -28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers -28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesString -28: [ OK ] CommandLineParserTest.HandlesString (0 ms) -28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues -28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix -28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers -28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown -28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) -28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault -28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) -28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments -28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) -28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions -28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) -28: [----------] 13 tests from CommandLineParserTest (0 ms total) -28: -28: [----------] 6 tests from CommandLineProgramContextTest -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) -28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) -28: -28: [----------] 3 tests from OutputNamesTest -28: [ RUN ] OutputNamesTest.CanBeSuffixed -28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) -28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend -28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) -28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded -28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) -28: [----------] 3 tests from OutputNamesTest (0 ms total) -28: -28: [----------] 22 tests from ParseCommonArgsTest -28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs -28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args -28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs -28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs -28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs -28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum -28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs -28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs -28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit -28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs -28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs -28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults -28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName -28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension -28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles -28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles -28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) -28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified -28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles -28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (38 ms) -28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension -28: Value is /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo -28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) -28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile -28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) -28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName -28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (54 ms) -28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs -28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) -28: [----------] 22 tests from ParseCommonArgsTest (94 ms total) -28: -28: [----------] Global test environment tear-down -28: [==========] 60 tests from 7 test suites ran. (149 ms total) -28: [ PASSED ] 60 tests. -28/92 Test #28: CommandLineUnitTests ...................... Passed 0.16 sec -test 29 - Start 29: DomDecTests - -29: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/DomDecTests.xml" -29: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests -29: Test timeout computed to be: 30 -29: [==========] Running 9 tests from 2 test suites. -29: [----------] Global test environment set-up. -29: [----------] 7 tests from HashedMap -29: [ RUN ] HashedMap.InsertsFinds -29: [ OK ] HashedMap.InsertsFinds (0 ms) -29: [ RUN ] HashedMap.NegativeKeysWork -29: [ OK ] HashedMap.NegativeKeysWork (0 ms) -29: [ RUN ] HashedMap.InsertsErases -29: [ OK ] HashedMap.InsertsErases (0 ms) -29: [ RUN ] HashedMap.InsertsOrAssigns -29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) -29: [ RUN ] HashedMap.Clears -29: [ OK ] HashedMap.Clears (0 ms) -29: [ RUN ] HashedMap.LinkedEntries -29: [ OK ] HashedMap.LinkedEntries (0 ms) -29: [ RUN ] HashedMap.ResizesTable -29: [ OK ] HashedMap.ResizesTable (0 ms) -29: [----------] 7 tests from HashedMap (0 ms total) -29: -29: [----------] 2 tests from LocalAtomSetManager -29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet -29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) -29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices -29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) -29: [----------] 2 tests from LocalAtomSetManager (0 ms total) -29: -29: [----------] Global test environment tear-down -29: [==========] 9 tests from 2 test suites ran. (0 ms total) -29: [ PASSED ] 9 tests. -29/92 Test #29: DomDecTests ............................... Passed 0.01 sec -test 30 - Start 30: DomDecMpiTests - -30: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/DomDecMpiTests.xml" -30: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/domdec/tests -30: Test timeout computed to be: 30 -30: [==========] Running 4 tests from 1 test suite. -30: [----------] Global test environment set-up. -30: [----------] 4 tests from HaloExchangeTest -30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse -30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses -30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim -30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 -30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) -30: [----------] 4 tests from HaloExchangeTest (1 ms total) -30: -30: [----------] Global test environment tear-down -30: [==========] 4 tests from 1 test suite ran. (1 ms total) -30: [ PASSED ] 4 tests. -30/92 Test #30: DomDecMpiTests ............................ Passed 0.03 sec -test 31 - Start 31: EwaldUnitTests - -31: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/EwaldUnitTests.xml" -31: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/ewald/tests -31: Test timeout computed to be: 30 -31: [==========] Running 407 tests from 9 test suites. -31: [----------] Global test environment set-up. -31: [----------] 6 tests from SeparatePmeRanksPermittedTest -31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons -31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled -31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag -31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) -31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) -31: -31: [----------] 108 tests from Pme_SplineAndSpreadTest -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (28 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [----------] 108 tests from Pme_SplineAndSpreadTest (110 ms total) -31: -31: [----------] 64 tests from Pme_SolveTest -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [----------] 64 tests from Pme_SolveTest (14 ms total) -31: -31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (5 ms total) -31: -31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (7 ms total) -31: -31: [----------] 64 tests from PmeDiffEps_SolveTest -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [----------] 64 tests from PmeDiffEps_SolveTest (11 ms total) -31: -31: [----------] 72 tests from Pme_GatherTest -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (19 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (4 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [----------] 72 tests from Pme_GatherTest (40 ms total) -31: -31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) -31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) -31: -31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (103 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (66 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (73 ms) -31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (273 ms total) -31: -31: [----------] Global test environment tear-down -31: [==========] 407 tests from 9 test suites ran. (466 ms total) -31: [ PASSED ] 311 tests. -31: [ SKIPPED ] 96 tests, listed below: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31/92 Test #31: EwaldUnitTests ............................ Passed 0.50 sec -test 32 - Start 32: FFTUnitTests - -32: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/FFTUnitTests.xml" -32: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/fft/tests -32: Test timeout computed to be: 1920 -32: [==========] Running 15 tests from 4 test suites. -32: [----------] Global test environment set-up. -32: [----------] 2 tests from ManyFFTTest -32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test -32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (4 ms) -32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test -32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (13 ms) -32: [----------] 2 tests from ManyFFTTest (18 ms total) -32: -32: [----------] 1 test from FFTTest -32: [ RUN ] FFTTest.Real2DLength18_15Test -32: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) -32: [----------] 1 test from FFTTest (3 ms total) -32: -32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (10 ms) -32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (25 ms total) -32: -32: [----------] 2 tests from Works/ParameterizedFFTTest3D -32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 -32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) -32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 -32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) -32: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) -32: -32: [----------] Global test environment tear-down -32: [==========] 15 tests from 4 test suites ran. (49 ms total) -32: [ PASSED ] 15 tests. -32/92 Test #32: FFTUnitTests .............................. Passed 0.08 sec -test 33 - Start 33: GpuUtilsUnitTests - -33: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" -33: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gpu_utils/tests -33: Test timeout computed to be: 30 -33: [==========] Running 67 tests from 22 test suites. -33: [----------] Global test environment set-up. -33: [----------] 2 tests from ClfftInitializer -33: [ RUN ] ClfftInitializer.SingleInitializationWorks -33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) -33: [ RUN ] ClfftInitializer.TwoInitializationsWork -33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) -33: [----------] 2 tests from ClfftInitializer (0 ms total) -33: -33: [----------] 1 test from DevicesAvailable -33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice -33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) -33: [----------] 1 test from DevicesAvailable (0 ms total) -33: -33: [----------] 1 test from DeviceStreamManagerTest -33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice -33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) -33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int -33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float -33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly -33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float -33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector -33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.Swap -33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.Comparison -33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float -33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector -33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.Swap -33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.Comparison -33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector -33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.Swap -33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.Comparison -33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly -33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector -33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.Swap -33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.Comparison -33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) -33: -33: [----------] 1 test from HostAllocatorUntypedTest -33: [ RUN ] HostAllocatorUntypedTest.Comparison -33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) -33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.Move -33: [ OK ] AllocatorTest/0.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/0 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.Move -33: [ OK ] AllocatorTest/1.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/1 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> -33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.Move -33: [ OK ] AllocatorTest/2.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/2 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.Move -33: [ OK ] AllocatorTest/3.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/3 (0 ms total) -33: -33: [----------] Global test environment tear-down -33: [==========] 67 tests from 22 test suites ran. (1 ms total) -33: [ PASSED ] 67 tests. -33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.13 sec -test 34 - Start 34: HardwareUnitTests - -34: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/HardwareUnitTests.xml" -34: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/hardware/tests -34: Test timeout computed to be: 30 -34: [==========] Running 22 tests from 10 test suites. -34: [----------] Global test environment set-up. -34: [----------] 1 test from CpuInfoTest -34: [ RUN ] CpuInfoTest.SupportLevel -34: [ OK ] CpuInfoTest.SupportLevel (7 ms) -34: [----------] 1 test from CpuInfoTest (7 ms total) -34: -34: [----------] 4 tests from HardwareTopologyTest -34: [ RUN ] HardwareTopologyTest.Execute -34: [ OK ] HardwareTopologyTest.Execute (17 ms) -34: [ RUN ] HardwareTopologyTest.HwlocExecute -34: [ OK ] HardwareTopologyTest.HwlocExecute (14 ms) -34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency -34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms) -34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency -34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (15 ms) -34: [----------] 4 tests from HardwareTopologyTest (68 ms total) -34: -34: [----------] 1 test from DevicesManagerTest -34: [ RUN ] DevicesManagerTest.Serialization -34: [ OK ] DevicesManagerTest.Serialization (0 ms) -34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid -34: [----------] 1 test from DevicesManagerTest (0 ms total) -34: -34: [----------] 1 test from UuidStringTest -34: [ RUN ] UuidStringTest.Works -34: [ OK ] UuidStringTest.Works (0 ms) -34: [----------] 1 test from UuidStringTest (0 ms total) -34: -34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (3 ms total) -34: -34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) -34: -34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest -34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) -34: -34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest -34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) -34: -34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest -34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) -34: -34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest -34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) -34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) -34: -34: [----------] Global test environment tear-down -34: [==========] 22 tests from 10 test suites ran. (89 ms total) -34: [ PASSED ] 22 tests. -34: -34: YOU HAVE 1 DISABLED TEST -34: -34/92 Test #34: HardwareUnitTests ......................... Passed 0.10 sec -test 35 - Start 35: MathUnitTests - -35: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MathUnitTests.xml" -35: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/math/tests -35: Test timeout computed to be: 30 -35: [==========] Running 328 tests from 41 test suites. -35: [----------] Global test environment set-up. -35: [----------] 1 test from EmptyArrayRefWithPaddingTest -35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty -35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) -35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) -35: -35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest -35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty -35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) -35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) -35: -35: [----------] 2 tests from InvertBoxMatrixTest -35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent -35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) -35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace -35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) -35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) -35: -35: [----------] 8 tests from ComplexNumberTest -35: [ RUN ] ComplexNumberTest.RealComplexMultiply -35: [ OK ] ComplexNumberTest.RealComplexMultiply (19 ms) -35: [ RUN ] ComplexNumberTest.RealComplexExp -35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexAdd -35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexSubtract -35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexMultiply -35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexDivision -35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexConjugate -35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexAbs2 -35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) -35: [----------] 8 tests from ComplexNumberTest (20 ms total) -35: -35: [----------] 11 tests from TranslateAndScaleTest -35: [ RUN ] TranslateAndScaleTest.identityTransformation -35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling -35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation -35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial -35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector -35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingIdentity -35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial -35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector -35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero -35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero -35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector -35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) -35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) -35: -35: [----------] 3 tests from AffineTransformationTest -35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors -35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) -35: [ RUN ] AffineTransformationTest.applyTransformationToVectors -35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) -35: [ RUN ] AffineTransformationTest.retrieveGradient -35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) -35: [----------] 3 tests from AffineTransformationTest (0 ms total) -35: -35: [----------] 14 tests from DensitySimilarityTest -35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect -35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect -35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch -35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) -35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch -35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) -35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect -35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero -35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect -35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect -35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne -35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (18 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated -35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (16 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated -35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect -35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.NormalizationCorrect -35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive -35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) -35: [----------] 14 tests from DensitySimilarityTest (36 ms total) -35: -35: [----------] 6 tests from StructureSimilarityTest -35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD -35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) -35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho -35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD -35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho -35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex -35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex -35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) -35: [----------] 6 tests from StructureSimilarityTest (0 ms total) -35: -35: [----------] 8 tests from ExponentialMovingAverage -35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero -35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) -35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative -35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) -35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue -35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) -35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue -35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) -35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly -35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) -35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing -35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) -35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect -35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) -35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree -35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) -35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) -35: -35: [----------] 21 tests from FunctionTest -35: [ RUN ] FunctionTest.StaticLog2 -35: [ OK ] FunctionTest.StaticLog2 (0 ms) -35: [ RUN ] FunctionTest.Log2I32Bit -35: [ OK ] FunctionTest.Log2I32Bit (0 ms) -35: [ RUN ] FunctionTest.Log2I64Bit -35: [ OK ] FunctionTest.Log2I64Bit (0 ms) -35: [ RUN ] FunctionTest.GreatestCommonDivisor -35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) -35: [ RUN ] FunctionTest.InvsqrtFloat -35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) -35: [ RUN ] FunctionTest.InvsqrtDouble -35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) -35: [ RUN ] FunctionTest.InvsqrtInteger -35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) -35: [ RUN ] FunctionTest.InvcbrtFloat -35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) -35: [ RUN ] FunctionTest.InvcbrtDouble -35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) -35: [ RUN ] FunctionTest.InvcbrtInteger -35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) -35: [ RUN ] FunctionTest.SixthrootFloat -35: [ OK ] FunctionTest.SixthrootFloat (0 ms) -35: [ RUN ] FunctionTest.SixthrootDouble -35: [ OK ] FunctionTest.SixthrootDouble (0 ms) -35: [ RUN ] FunctionTest.SixthrootInteger -35: [ OK ] FunctionTest.SixthrootInteger (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootFloat -35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootDouble -35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootInteger -35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) -35: [ RUN ] FunctionTest.Powers -35: [ OK ] FunctionTest.Powers (0 ms) -35: [ RUN ] FunctionTest.ErfInvFloat -35: [ OK ] FunctionTest.ErfInvFloat (0 ms) -35: [ RUN ] FunctionTest.ErfInvDouble -35: [ OK ] FunctionTest.ErfInvDouble (0 ms) -35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat -35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) -35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble -35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) -35: [----------] 21 tests from FunctionTest (1 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char -35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char -35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short -35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short -35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int -35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int -35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long -35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long -35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) -35: -35: [----------] 4 tests from GaussianOn1DLattice -35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne -35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) -35: [ RUN ] GaussianOn1DLattice.isCorrect -35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) -35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero -35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) -35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange -35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) -35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) -35: -35: [----------] 9 tests from GaussTransformTest -35: [ RUN ] GaussTransformTest.isZeroUponConstruction -35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) -35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss -35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) -35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero -35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) -35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero -35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) -35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues -35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) -35: [ RUN ] GaussTransformTest.view -35: [ OK ] GaussTransformTest.view (0 ms) -35: [----------] 9 tests from GaussTransformTest (0 ms total) -35: -35: [----------] 3 tests from DensityFittingForce -35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity -35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) -35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections -35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) -35: [ RUN ] DensityFittingForce.pullsTowardsDerivative -35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) -35: [----------] 3 tests from DensityFittingForce (0 ms total) -35: -35: [----------] 2 tests from InvertMatrixTest -35: [ RUN ] InvertMatrixTest.IdentityIsImpotent -35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) -35: [ RUN ] InvertMatrixTest.ComputesInverse -35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) -35: [----------] 2 tests from InvertMatrixTest (0 ms total) -35: -35: [----------] 22 tests from MatrixTest -35: [ RUN ] MatrixTest.canSetFromArray -35: [ OK ] MatrixTest.canSetFromArray (0 ms) -35: [ RUN ] MatrixTest.canSetStaticallyFromList -35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) -35: [ RUN ] MatrixTest.canConstructAndFill -35: [ OK ] MatrixTest.canConstructAndFill (0 ms) -35: [ RUN ] MatrixTest.canSetValues -35: [ OK ] MatrixTest.canSetValues (0 ms) -35: [ RUN ] MatrixTest.canCopyAssign -35: [ OK ] MatrixTest.canCopyAssign (0 ms) -35: [ RUN ] MatrixTest.canSwap -35: [ OK ] MatrixTest.canSwap (0 ms) -35: [ RUN ] MatrixTest.staticMultiDimArrayExtent -35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) -35: [ RUN ] MatrixTest.canAddMatrix -35: [ OK ] MatrixTest.canAddMatrix (0 ms) -35: [ RUN ] MatrixTest.canSubstractMatrix -35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) -35: [ RUN ] MatrixTest.canNegateMatrix -35: [ OK ] MatrixTest.canNegateMatrix (0 ms) -35: [ RUN ] MatrixTest.determinantWorks -35: [ OK ] MatrixTest.determinantWorks (0 ms) -35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero -35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) -35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix -35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) -35: [ RUN ] MatrixTest.traceWorks -35: [ OK ] MatrixTest.traceWorks (0 ms) -35: [ RUN ] MatrixTest.transposeWorks -35: [ OK ] MatrixTest.transposeWorks (0 ms) -35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix -35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) -35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix -35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) -35: [ RUN ] MatrixTest.canFillLegacyMatrix -35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) -35: [ RUN ] MatrixTest.IdentityMatrix -35: [ OK ] MatrixTest.IdentityMatrix (0 ms) -35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct -35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) -35: [ RUN ] MatrixTest.MatrixMatrixMultiplication -35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) -35: [ RUN ] MatrixTest.MatrixVectorMultiplication -35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) -35: [----------] 22 tests from MatrixTest (0 ms total) -35: -35: [----------] 25 tests from MultiDimArrayTest -35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic -35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic -35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic -35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic -35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic -35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic -35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic -35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic -35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic -35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic -35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic -35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic -35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSwapStatic -35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSwapDynamic -35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent -35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) -35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray -35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) -35: [ RUN ] MultiDimArrayTest.conversionToView -35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) -35: [ RUN ] MultiDimArrayTest.conversionToConstView -35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) -35: [ RUN ] MultiDimArrayTest.viewBegin -35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) -35: [ RUN ] MultiDimArrayTest.viewEnd -35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) -35: [ RUN ] MultiDimArrayTest.constViewConstBegin -35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) -35: [ RUN ] MultiDimArrayTest.constViewConstEnd -35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) -35: [----------] 25 tests from MultiDimArrayTest (0 ms total) -35: -35: [----------] 4 tests from MultiDimArrayToMdSpanTest -35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) -35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) -35: -35: [----------] 9 tests from NelderMeadSimplexTest -35: [ RUN ] NelderMeadSimplexTest.BestVertex -35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) -35: [ RUN ] NelderMeadSimplexTest.WorstVertex -35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) -35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue -35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) -35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint -35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint -35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint -35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst -35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) -35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest -35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) -35: [ RUN ] NelderMeadSimplexTest.OrientedLength -35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) -35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) -35: -35: [----------] 2 tests from NelderMead -35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly -35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) -35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly -35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) -35: [----------] 2 tests from NelderMead (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ResizeWorks -35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ReserveWorks -35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanCopyAssign -35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanMoveAssign -35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanSwap -35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ResizeWorks -35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ReserveWorks -35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanCopyAssign -35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanMoveAssign -35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanSwap -35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ResizeWorks -35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ReserveWorks -35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanCopyAssign -35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanMoveAssign -35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanSwap -35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > -35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ResizeWorks -35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ReserveWorks -35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanCopyAssign -35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanMoveAssign -35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanSwap -35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > -35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ResizeWorks -35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ReserveWorks -35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanCopyAssign -35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanMoveAssign -35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanSwap -35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ResizeWorks -35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ReserveWorks -35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanCopyAssign -35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanMoveAssign -35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanSwap -35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ResizeWorks -35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ReserveWorks -35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanCopyAssign -35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanMoveAssign -35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanSwap -35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ResizeWorks -35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ReserveWorks -35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanCopyAssign -35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanMoveAssign -35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanSwap -35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ResizeWorks -35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ReserveWorks -35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanCopyAssign -35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanMoveAssign -35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanSwap -35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ResizeWorks -35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ReserveWorks -35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanCopyAssign -35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanMoveAssign -35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanSwap -35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) -35: -35: [----------] 41 tests from RVecTest -35: [ RUN ] RVecTest.CanBeStoredInVector -35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) -35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec -35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) -35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec -35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) -35: [ RUN ] RVecTest.WorksAsMutable_rvec -35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) -35: [ RUN ] RVecTest.WorksAs_rvec_Array -35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) -35: [ RUN ] RVecTest.ComparesEqual -35: [ OK ] RVecTest.ComparesEqual (0 ms) -35: [ RUN ] RVecTest.ComparesUnequal -35: [ OK ] RVecTest.ComparesUnequal (0 ms) -35: [ RUN ] RVecTest.CanAddRVecToRvec -35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) -35: [ RUN ] RVecTest.CanAddAssignRVecToRvec -35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) -35: [ RUN ] RVecTest.CanSubtractRVecFromRvec -35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) -35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec -35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) -35: [ RUN ] RVecTest.CanDotProductRVecByRvec -35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) -35: [ RUN ] RVecTest.CanCrossProductRVecByRvec -35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) -35: [ RUN ] RVecTest.CanDivideRVecInplace -35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) -35: [ RUN ] RVecTest.CanScaleRVec -35: [ OK ] RVecTest.CanScaleRVec (0 ms) -35: [ RUN ] RVecTest.CanDivideRVec -35: [ OK ] RVecTest.CanDivideRVec (0 ms) -35: [ RUN ] RVecTest.CanDoUnitvFromRVec -35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) -35: [ RUN ] RVecTest.CanSqLengthOfRVec -35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanLengthOfRVec -35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanCastToRVec -35: [ OK ] RVecTest.CanCastToRVec (0 ms) -35: [ RUN ] RVecTest.CanCastToDVec -35: [ OK ] RVecTest.CanCastToDVec (0 ms) -35: [ RUN ] RVecTest.CanLeftScalarMultiply -35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) -35: [ RUN ] RVecTest.CanRightScalarMultiply -35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) -35: [ RUN ] RVecTest.CanGetUnitvFromRVec -35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) -35: [ RUN ] RVecTest.CanGetSqLengthOfRVec -35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanGetLengthOfRVec -35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanDoCrossProductOfRVec -35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) -35: [ RUN ] RVecTest.CanDoDotProductOfRVec -35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) -35: [ RUN ] RVecTest.CanScaleByVector -35: [ OK ] RVecTest.CanScaleByVector (0 ms) -35: [ RUN ] RVecTest.CanNegate -35: [ OK ] RVecTest.CanNegate (0 ms) -35: [ RUN ] RVecTest.asIVec -35: [ OK ] RVecTest.asIVec (0 ms) -35: [ RUN ] RVecTest.elementWiseMin -35: [ OK ] RVecTest.elementWiseMin (0 ms) -35: [ RUN ] RVecTest.elementWiseMax -35: [ OK ] RVecTest.elementWiseMax (0 ms) -35: [ RUN ] RVecTest.WorksAs_dvec_Reference -35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) -35: [ RUN ] RVecTest.WorksAs_ivec_Reference -35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) -35: [ RUN ] RVecTest.WorksAs_rvec_Reference -35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) -35: [ RUN ] RVecTest.CopyConstructorWorks -35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) -35: [ RUN ] RVecTest.CopyAssignmentWorks -35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) -35: [ RUN ] RVecTest.MoveConstructorWorks -35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) -35: [ RUN ] RVecTest.MoveAssignmentWorks -35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) -35: [ RUN ] RVecTest.UsableInConstexpr -35: [ OK ] RVecTest.UsableInConstexpr (0 ms) -35: [----------] 41 tests from RVecTest (0 ms total) -35: -35: [----------] Global test environment tear-down -35: [==========] 328 tests from 41 test suites ran. (61 ms total) -35: [ PASSED ] 328 tests. -35/92 Test #35: MathUnitTests ............................. Passed 0.08 sec -test 36 - Start 36: MdrunUtilityUnitTests - -36: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" -36: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests -36: Test timeout computed to be: 30 -36: [==========] Running 21 tests from 2 test suites. -36: [----------] Global test environment set-up. -36: [----------] 4 tests from MDModulesNotifierTest -36: [ RUN ] MDModulesNotifierTest.AddConsumer -36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter -36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers -36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources -36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) -36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) -36: -36: [----------] 17 tests from ThreadAffinityTest -36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled -36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported -36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware -36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread -36: NOTE: Affinity setting failed. -36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto -36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced -36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads -36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing -36: NOTE: Affinity setting for 1/2 threads failed. -36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) -36: [----------] 17 tests from ThreadAffinityTest (2 ms total) -36: -36: [----------] Global test environment tear-down -36: [==========] 21 tests from 2 test suites ran. (3 ms total) -36: [ PASSED ] 21 tests. -36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.07 sec -test 37 - Start 37: MdrunUtilityMpiUnitTests - -37: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" -37: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdrunutility/tests -37: Test timeout computed to be: 30 -37: [==========] Running 13 tests from 2 test suites. -37: [----------] Global test environment set-up. -37: [----------] 6 tests from ThreadAffinityMultiRankTest -37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode -37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride -37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes -37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled -37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto -37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce -37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) -37: [----------] 6 tests from ThreadAffinityMultiRankTest (5 ms total) -37: -37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) -37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (5 ms total) -37: -37: [----------] Global test environment tear-down -37: [==========] 13 tests from 2 test suites ran. (11 ms total) -37: [ PASSED ] 13 tests. -37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 0.10 sec -test 38 - Start 38: MDSpanTests - -38: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MDSpanTests.xml" -38: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdspan/tests -38: Test timeout computed to be: 30 -38: [==========] Running 32 tests from 7 test suites. -38: [----------] Global test environment set-up. -38: [----------] 4 tests from BasicAccessorPolicy -38: [ RUN ] BasicAccessorPolicy.Decay -38: [ OK ] BasicAccessorPolicy.Decay (0 ms) -38: [ RUN ] BasicAccessorPolicy.Access -38: [ OK ] BasicAccessorPolicy.Access (0 ms) -38: [ RUN ] BasicAccessorPolicy.Offset -38: [ OK ] BasicAccessorPolicy.Offset (0 ms) -38: [ RUN ] BasicAccessorPolicy.CopyAccessor -38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) -38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) -38: -38: [----------] 4 tests from ExtentsTest -38: [ RUN ] ExtentsTest.Construction -38: [ OK ] ExtentsTest.Construction (0 ms) -38: [ RUN ] ExtentsTest.PurelyStatic -38: [ OK ] ExtentsTest.PurelyStatic (0 ms) -38: [ RUN ] ExtentsTest.RankNought -38: [ OK ] ExtentsTest.RankNought (0 ms) -38: [ RUN ] ExtentsTest.Assignment -38: [ OK ] ExtentsTest.Assignment (0 ms) -38: [----------] 4 tests from ExtentsTest (0 ms total) -38: -38: [----------] 8 tests from MdSpanExtension -38: [ RUN ] MdSpanExtension.SlicingAllStatic -38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) -38: [ RUN ] MdSpanExtension.SlicingDynamic -38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) -38: [ RUN ] MdSpanExtension.SlicingAllStatic3D -38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) -38: [ RUN ] MdSpanExtension.SlicingEqualsView3D -38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) -38: [ RUN ] MdSpanExtension.additionWorks -38: [ OK ] MdSpanExtension.additionWorks (0 ms) -38: [ RUN ] MdSpanExtension.subtractionWorks -38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) -38: [ RUN ] MdSpanExtension.multiplicationWorks -38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) -38: [ RUN ] MdSpanExtension.divisionWorks -38: [ OK ] MdSpanExtension.divisionWorks (0 ms) -38: [----------] 8 tests from MdSpanExtension (0 ms total) -38: -38: [----------] 3 tests from LayoutTests -38: [ RUN ] LayoutTests.LayoutRightConstruction -38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) -38: [ RUN ] LayoutTests.LayoutRightProperties -38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) -38: [ RUN ] LayoutTests.LayoutRightOperator -38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) -38: [----------] 3 tests from LayoutTests (0 ms total) -38: -38: [----------] 1 test from MdSpanTest -38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly -38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) -38: [----------] 1 test from MdSpanTest (0 ms total) -38: -38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -38: [ RUN ] MdSpanTest/0.Rank -38: [ OK ] MdSpanTest/0.Rank (0 ms) -38: [ RUN ] MdSpanTest/0.DynamicRank -38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) -38: [ RUN ] MdSpanTest/0.Extents -38: [ OK ] MdSpanTest/0.Extents (0 ms) -38: [ RUN ] MdSpanTest/0.Strides -38: [ OK ] MdSpanTest/0.Strides (0 ms) -38: [ RUN ] MdSpanTest/0.Properties -38: [ OK ] MdSpanTest/0.Properties (0 ms) -38: [ RUN ] MdSpanTest/0.Operator -38: [ OK ] MdSpanTest/0.Operator (0 ms) -38: [----------] 6 tests from MdSpanTest/0 (0 ms total) -38: -38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -38: [ RUN ] MdSpanTest/1.Rank -38: [ OK ] MdSpanTest/1.Rank (0 ms) -38: [ RUN ] MdSpanTest/1.DynamicRank -38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) -38: [ RUN ] MdSpanTest/1.Extents -38: [ OK ] MdSpanTest/1.Extents (0 ms) -38: [ RUN ] MdSpanTest/1.Strides -38: [ OK ] MdSpanTest/1.Strides (0 ms) -38: [ RUN ] MdSpanTest/1.Properties -38: [ OK ] MdSpanTest/1.Properties (0 ms) -38: [ RUN ] MdSpanTest/1.Operator -38: [ OK ] MdSpanTest/1.Operator (0 ms) -38: [----------] 6 tests from MdSpanTest/1 (0 ms total) -38: -38: [----------] Global test environment tear-down -38: [==========] 32 tests from 7 test suites ran. (0 ms total) -38: [ PASSED ] 32 tests. -38/92 Test #38: MDSpanTests ............................... Passed 0.11 sec -test 39 - Start 39: MdtypesUnitTest - -39: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdtypesUnitTest.xml" -39: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/mdtypes/tests -39: Test timeout computed to be: 30 -39: [==========] Running 97 tests from 7 test suites. -39: [----------] Global test environment set-up. -39: [----------] 4 tests from ForeingLambdaTermsDhdl -39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks -39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear -39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative -39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul -39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) -39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) -39: -39: [----------] 4 tests from ObservablesReducerTest -39: [ RUN ] ObservablesReducerTest.CanMoveAssign -39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) -39: [ RUN ] ObservablesReducerTest.CanMoveConstruct -39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) -39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers -39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) -39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber -39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) -39: [----------] 4 tests from ObservablesReducerTest (0 ms total) -39: -39: [----------] 2 tests from CheckpointDataTest -39: [ RUN ] CheckpointDataTest.SingleDataTest -39: [ OK ] CheckpointDataTest.SingleDataTest (815 ms) -39: [ RUN ] CheckpointDataTest.MultiDataTest -39: [ OK ] CheckpointDataTest.MultiDataTest (1783 ms) -39: [----------] 2 tests from CheckpointDataTest (2599 ms total) -39: -39: [----------] 7 tests from ForceBuffers -39: [ RUN ] ForceBuffers.ConstructsUnpinned -39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) -39: [ RUN ] ForceBuffers.ConstructsPinned -39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) -39: [ RUN ] ForceBuffers.ConstructsEmpty -39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) -39: [ RUN ] ForceBuffers.ResizeWorks -39: [ OK ] ForceBuffers.ResizeWorks (0 ms) -39: [ RUN ] ForceBuffers.PaddingWorks -39: [ OK ] ForceBuffers.PaddingWorks (0 ms) -39: [ RUN ] ForceBuffers.CopyWorks -39: [ OK ] ForceBuffers.CopyWorks (0 ms) -39: [ RUN ] ForceBuffers.CopyDoesNotPin -39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) -39: [----------] 7 tests from ForceBuffers (0 ms total) -39: -39: [----------] 5 tests from MultipleTimeStepping -39: [ RUN ] MultipleTimeStepping.ChecksNumLevels -39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) -39: [ RUN ] MultipleTimeStepping.SelectsForceGroups -39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksStepFactor -39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel -39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksIntegrator -39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) -39: [----------] 5 tests from MultipleTimeStepping (0 ms total) -39: -39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) -39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) -39: -39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) -39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) -39: -39: [----------] Global test environment tear-down -39: [==========] 97 tests from 7 test suites ran. (2601 ms total) -39: [ PASSED ] 97 tests. -39/92 Test #39: MdtypesUnitTest ........................... Passed 2.61 sec -test 40 - Start 40: OnlineHelpUnitTests - -40: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" -40: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/onlinehelp/tests -40: Test timeout computed to be: 30 -40: [==========] Running 22 tests from 4 test suites. -40: [----------] Global test environment set-up. -40: [----------] 6 tests from TextTableFormatterTest -40: [ RUN ] TextTableFormatterTest.HandlesBasicCase -40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles -40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesIndentation -40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines -40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding -40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns -40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) -40: [----------] 6 tests from TextTableFormatterTest (0 ms total) -40: -40: [----------] 3 tests from HelpManagerTest -40: [ RUN ] HelpManagerTest.HandlesRootTopic -40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) -40: [ RUN ] HelpManagerTest.HandlesSubTopics -40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) -40: [ RUN ] HelpManagerTest.HandlesInvalidTopics -40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) -40: [----------] 3 tests from HelpManagerTest (0 ms total) -40: -40: [----------] 2 tests from HelpTopicFormattingTest -40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic -40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) -40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics -40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) -40: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) -40: -40: [----------] 11 tests from HelpWriterContextTest -40: [ RUN ] HelpWriterContextTest.FormatsParagraphs -40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs -40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) -40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace -40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralText -40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning -40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation -40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsBulletList -40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList -40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable -40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsGridTable -40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsTitles -40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) -40: [----------] 11 tests from HelpWriterContextTest (1 ms total) -40: -40: [----------] Global test environment tear-down -40: [==========] 22 tests from 4 test suites ran. (3 ms total) -40: [ PASSED ] 22 tests. -40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.02 sec -test 41 - Start 41: OptionsUnitTests - -41: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/OptionsUnitTests.xml" -41: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/options/tests -41: Test timeout computed to be: 30 -41: [==========] Running 112 tests from 18 test suites. -41: [----------] Global test environment set-up. -41: [----------] 5 tests from AbstractOptionStorageTest -41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish -41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval -41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition -41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition -41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) -41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues -41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) -41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) -41: -41: [----------] 10 tests from FileNameOptionTest -41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue -41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption -41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension -41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix -41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) -41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix -41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue -41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) -41: [----------] 10 tests from FileNameOptionTest (0 ms total) -41: -41: [----------] 16 tests from FileNameOptionManagerTest -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension -41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking -41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile -41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) -41: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) -41: -41: [----------] 1 test from OptionsTest -41: [ RUN ] OptionsTest.FailsOnNonsafeStorage -41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) -41: [----------] 1 test from OptionsTest (0 ms total) -41: -41: [----------] 9 tests from OptionsAssignerTest -41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter -41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue -41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter -41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter -41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMissingValue -41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesExtraValue -41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesGroups -41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesSections -41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources -41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) -41: [----------] 9 tests from OptionsAssignerTest (0 ms total) -41: -41: [----------] 4 tests from OptionsAssignerBooleanTest -41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue -41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue -41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo -41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue -41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) -41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) -41: -41: [----------] 13 tests from OptionsAssignerIntegerTest -41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue -41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow -41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue -41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet -41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet -41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues -41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector -41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) -41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) -41: -41: [----------] 5 tests from OptionsAssignerDoubleTest -41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue -41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat -41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) -41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) -41: -41: [----------] 9 tests from OptionsAssignerStringTest -41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue -41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray -41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue -41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue -41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) -41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) -41: -41: [----------] 6 tests from OptionsAssignerEnumTest -41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue -41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues -41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange -41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) -41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) -41: -41: [----------] 8 tests from RepeatingOptionSectionTest -41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance -41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption -41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance -41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue -41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances -41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault -41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault -41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections -41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) -41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) -41: -41: [----------] 1 test from TimeUnitManagerTest -41: [ RUN ] TimeUnitManagerTest.BasicOperations -41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) -41: [----------] 1 test from TimeUnitManagerTest (0 ms total) -41: -41: [----------] 4 tests from TimeUnitBehaviorTest -41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue -41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues -41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources -41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks -41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) -41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) -41: -41: [----------] 2 tests from TreeValueSupportAssignTest -41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree -41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) -41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays -41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) -41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) -41: -41: [----------] 1 test from TreeValueSupportAssignErrorTest -41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue -41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) -41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) -41: -41: [----------] 5 tests from TreeValueSupportCheckTest -41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty -41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree -41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 -41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 -41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue -41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) -41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) -41: -41: [----------] 6 tests from TreeValueSupportAdjustTest -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues -41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues -41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues -41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) -41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) -41: -41: [----------] 7 tests from TreeValueSupportTest -41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption -41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption -41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsInt64Option -41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsStringOption -41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsFloatOption -41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption -41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsEnumOption -41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) -41: [----------] 7 tests from TreeValueSupportTest (1 ms total) -41: -41: [----------] Global test environment tear-down -41: [==========] 112 tests from 18 test suites ran. (4 ms total) -41: [ PASSED ] 112 tests. -41/92 Test #41: OptionsUnitTests .......................... Passed 0.02 sec -test 42 - Start 42: PbcutilUnitTest - -42: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/PbcutilUnitTest.xml" -42: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/pbcutil/tests -42: Test timeout computed to be: 30 -42: [==========] Running 37 tests from 5 test suites. -42: [----------] Global test environment set-up. -42: [----------] 1 test from ShiftTest -42: [ RUN ] ShiftTest.CoordinateShiftWorks -42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) -42: [----------] 1 test from ShiftTest (0 ms total) -42: -42: [----------] 2 tests from MShift -42: [ RUN ] MShift.shiftsAndUnshifts -42: [ OK ] MShift.shiftsAndUnshifts (0 ms) -42: [ RUN ] MShift.shiftsAndUnshiftsSelf -42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) -42: [----------] 2 tests from MShift (0 ms total) -42: -42: [----------] 5 tests from PbcTest -42: [ RUN ] PbcTest.CalcShiftsWorks -42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) -42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox -42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox -42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox -42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf -42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) -42: [----------] 5 tests from PbcTest (0 ms total) -42: -42: [----------] 2 tests from PbcEnumsTest -42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect -42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) -42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect -42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) -42: [----------] 2 tests from PbcEnumsTest (0 ms total) -42: -42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) -42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (6 ms total) -42: -42: [----------] Global test environment tear-down -42: [==========] 37 tests from 5 test suites ran. (6 ms total) -42: [ PASSED ] 37 tests. -42/92 Test #42: PbcutilUnitTest ........................... Passed 0.02 sec -test 43 - Start 43: RandomUnitTests - -43: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/RandomUnitTests.xml" -43: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/random/tests -43: Test timeout computed to be: 30 -43: [==========] Running 44 tests from 10 test suites. -43: [----------] Global test environment set-up. -43: [----------] 4 tests from ExponentialDistributionTest -43: [ RUN ] ExponentialDistributionTest.Output -43: [ OK ] ExponentialDistributionTest.Output (0 ms) -43: [ RUN ] ExponentialDistributionTest.Logical -43: [ OK ] ExponentialDistributionTest.Logical (0 ms) -43: [ RUN ] ExponentialDistributionTest.Reset -43: [ OK ] ExponentialDistributionTest.Reset (0 ms) -43: [ RUN ] ExponentialDistributionTest.AltParam -43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) -43: -43: [----------] 4 tests from GammaDistributionTest -43: [ RUN ] GammaDistributionTest.Output -43: [ OK ] GammaDistributionTest.Output (0 ms) -43: [ RUN ] GammaDistributionTest.Logical -43: [ OK ] GammaDistributionTest.Logical (0 ms) -43: [ RUN ] GammaDistributionTest.Reset -43: [ OK ] GammaDistributionTest.Reset (0 ms) -43: [ RUN ] GammaDistributionTest.AltParam -43: [ OK ] GammaDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from GammaDistributionTest (0 ms total) -43: -43: [----------] 4 tests from NormalDistributionTest -43: [ RUN ] NormalDistributionTest.Output -43: [ OK ] NormalDistributionTest.Output (0 ms) -43: [ RUN ] NormalDistributionTest.Logical -43: [ OK ] NormalDistributionTest.Logical (0 ms) -43: [ RUN ] NormalDistributionTest.Reset -43: [ OK ] NormalDistributionTest.Reset (0 ms) -43: [ RUN ] NormalDistributionTest.AltParam -43: [ OK ] NormalDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from NormalDistributionTest (0 ms total) -43: -43: [----------] 1 test from SeedTest -43: [ RUN ] SeedTest.makeRandomSeed -43: [ OK ] SeedTest.makeRandomSeed (0 ms) -43: [----------] 1 test from SeedTest (0 ms total) -43: -43: [----------] 6 tests from TabulatedNormalDistributionTest -43: [ RUN ] TabulatedNormalDistributionTest.Output14 -43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Output16 -43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 -43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Logical -43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Reset -43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.AltParam -43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) -43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) -43: -43: [----------] 1 test from TabulatedNormalDistributionTableTest -43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties -43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) -43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) -43: -43: [----------] 6 tests from ThreeFry2x64Test -43: [ RUN ] ThreeFry2x64Test.Logical -43: [ OK ] ThreeFry2x64Test.Logical (0 ms) -43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence -43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) -43: [ RUN ] ThreeFry2x64Test.Reseed -43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) -43: [ RUN ] ThreeFry2x64Test.Discard -43: [ OK ] ThreeFry2x64Test.Discard (0 ms) -43: [ RUN ] ThreeFry2x64Test.InvalidCounter -43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) -43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter -43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) -43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) -43: -43: [----------] 4 tests from UniformIntDistributionTest -43: [ RUN ] UniformIntDistributionTest.Output -43: [ OK ] UniformIntDistributionTest.Output (0 ms) -43: [ RUN ] UniformIntDistributionTest.Logical -43: [ OK ] UniformIntDistributionTest.Logical (0 ms) -43: [ RUN ] UniformIntDistributionTest.Reset -43: [ OK ] UniformIntDistributionTest.Reset (0 ms) -43: [ RUN ] UniformIntDistributionTest.AltParam -43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) -43: -43: [----------] 5 tests from UniformRealDistributionTest -43: [ RUN ] UniformRealDistributionTest.GenerateCanonical -43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) -43: [ RUN ] UniformRealDistributionTest.Output -43: [ OK ] UniformRealDistributionTest.Output (0 ms) -43: [ RUN ] UniformRealDistributionTest.Logical -43: [ OK ] UniformRealDistributionTest.Logical (0 ms) -43: [ RUN ] UniformRealDistributionTest.Reset -43: [ OK ] UniformRealDistributionTest.Reset (0 ms) -43: [ RUN ] UniformRealDistributionTest.AltParam -43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) -43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) -43: -43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (7 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) -43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (8 ms total) -43: -43: [----------] Global test environment tear-down -43: [==========] 44 tests from 10 test suites ran. (10 ms total) -43: [ PASSED ] 44 tests. -43/92 Test #43: RandomUnitTests ........................... Passed 0.02 sec -test 44 - Start 44: RestraintTests - -44: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/RestraintTests.xml" -44: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/restraint/tests -44: Test timeout computed to be: 30 -44: [==========] Running 1 test from 1 test suite. -44: [----------] Global test environment set-up. -44: [----------] 1 test from RestraintManager -44: [ RUN ] RestraintManager.restraintList -44: [ OK ] RestraintManager.restraintList (0 ms) -44: [----------] 1 test from RestraintManager (0 ms total) -44: -44: [----------] Global test environment tear-down -44: [==========] 1 test from 1 test suite ran. (0 ms total) -44: [ PASSED ] 1 test. -44/92 Test #44: RestraintTests ............................ Passed 0.01 sec -test 45 - Start 45: TableUnitTests - -45: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TableUnitTests.xml" -45: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tables/tests -45: Test timeout computed to be: 30 -45: [==========] Running 20 tests from 2 test suites. -45: [----------] Global test environment set-up. -45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable -45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput -45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) -45: [ RUN ] SplineTableTest/0.Sinc -45: [ OK ] SplineTableTest/0.Sinc (0 ms) -45: [ RUN ] SplineTableTest/0.LJ12 -45: [ OK ] SplineTableTest/0.LJ12 (7 ms) -45: [ RUN ] SplineTableTest/0.PmeCorrection -45: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) -45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput -45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) -45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr -45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) -45: [ RUN ] SplineTableTest/0.TwoFunctions -45: [ OK ] SplineTableTest/0.TwoFunctions (12 ms) -45: [ RUN ] SplineTableTest/0.ThreeFunctions -45: [ OK ] SplineTableTest/0.ThreeFunctions (13 ms) -45: [ RUN ] SplineTableTest/0.Simd -45: [ OK ] SplineTableTest/0.Simd (2 ms) -45: [ RUN ] SplineTableTest/0.SimdTwoFunctions -45: [ OK ] SplineTableTest/0.SimdTwoFunctions (11 ms) -45: [----------] 10 tests from SplineTableTest/0 (49 ms total) -45: -45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable -45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput -45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) -45: [ RUN ] SplineTableTest/1.Sinc -45: [ OK ] SplineTableTest/1.Sinc (0 ms) -45: [ RUN ] SplineTableTest/1.LJ12 -45: [ OK ] SplineTableTest/1.LJ12 (0 ms) -45: [ RUN ] SplineTableTest/1.PmeCorrection -45: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) -45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput -45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) -45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr -45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) -45: [ RUN ] SplineTableTest/1.TwoFunctions -45: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) -45: [ RUN ] SplineTableTest/1.ThreeFunctions -45: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) -45: [ RUN ] SplineTableTest/1.Simd -45: [ OK ] SplineTableTest/1.Simd (0 ms) -45: [ RUN ] SplineTableTest/1.SimdTwoFunctions -45: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) -45: [----------] 10 tests from SplineTableTest/1 (9 ms total) -45: -45: [----------] Global test environment tear-down -45: [==========] 20 tests from 2 test suites ran. (58 ms total) -45: [ PASSED ] 20 tests. -45/92 Test #45: TableUnitTests ............................ Passed 0.07 sec -test 46 - Start 46: TaskAssignmentUnitTests - -46: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" -46: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment/tests -46: Test timeout computed to be: 30 -46: [==========] Running 3 tests from 2 test suites. -46: [----------] Global test environment set-up. -46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest -46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork -46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) -46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid -46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) -46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) -46: -46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest -46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow -46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) -46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) -46: -46: [----------] Global test environment tear-down -46: [==========] 3 tests from 2 test suites ran. (0 ms total) -46: [ PASSED ] 3 tests. -46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.01 sec -test 47 - Start 47: GmxTimingTests - -47: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxTimingTests.xml" -47: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/timing/tests -47: Test timeout computed to be: 30 -47: [==========] Running 6 tests from 1 test suite. -47: [----------] Global test environment set-up. -47: [----------] 6 tests from TimingTest -47: [ RUN ] TimingTest.ElementCountingWorks -47: [ OK ] TimingTest.ElementCountingWorks (0 ms) -47: [ RUN ] TimingTest.ElementNoCountingWorks -47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) -47: [ RUN ] TimingTest.SubElementCountingWorks -47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) -47: [ RUN ] TimingTest.SubElementNoCountingWorks -47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) -47: [ RUN ] TimingTest.RunWallCycle -47: [ OK ] TimingTest.RunWallCycle (1 ms) -47: [ RUN ] TimingTest.RunWallCycleSub -47: [ OK ] TimingTest.RunWallCycleSub (0 ms) -47: [----------] 6 tests from TimingTest (1 ms total) -47: -47: [----------] Global test environment tear-down -47: [==========] 6 tests from 1 test suite ran. (1 ms total) -47: [ PASSED ] 6 tests. -47/92 Test #47: GmxTimingTests ............................ Passed 0.01 sec -test 48 - Start 48: TopologyTest - -48: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TopologyTest.xml" -48: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/topology/tests -48: Test timeout computed to be: 30 -48: [==========] Running 153 tests from 10 test suites. -48: [----------] Global test environment set-up. -48: [----------] 3 tests from PdbAtomEntryTest -48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry -48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) -48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac -48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) -48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry -48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) -48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) -48: -48: [----------] 3 tests from ExclusionBlockTest -48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks -48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) -48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka -48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) -48: [ RUN ] ExclusionBlockTest.MergeExclusions -48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) -48: [----------] 3 tests from ExclusionBlockTest (0 ms total) -48: -48: [----------] 6 tests from InteractionListTest -48: [ RUN ] InteractionListTest.EmptyWorks -48: [ OK ] InteractionListTest.EmptyWorks (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionArray -48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms -48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionPointer -48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) -48: [ RUN ] InteractionListTest.CanAddListToOtherList -48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) -48: [ RUN ] InteractionListTest.ClearingWorks -48: [ OK ] InteractionListTest.ClearingWorks (0 ms) -48: [----------] 6 tests from InteractionListTest (0 ms total) -48: -48: [----------] 3 tests from IndexTest -48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) -48: [ RUN ] IndexTest.WriteIndexWorks -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.WriteIndexWorks (10 ms) -48: [ RUN ] IndexTest.WriteAndReadIndexWorks -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.WriteAndReadIndexWorks (3 ms) -48: [----------] 3 tests from IndexTest (16 ms total) -48: -48: [----------] 4 tests from MtopTest -48: [ RUN ] MtopTest.RangeBasedLoop -48: [ OK ] MtopTest.RangeBasedLoop (0 ms) -48: [ RUN ] MtopTest.Operators -48: [ OK ] MtopTest.Operators (0 ms) -48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms -48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) -48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly -48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) -48: [----------] 4 tests from MtopTest (0 ms total) -48: -48: [----------] 2 tests from IListRangeTest -48: [ RUN ] IListRangeTest.RangeBasedLoopWorks -48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) -48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction -48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) -48: [----------] 2 tests from IListRangeTest (0 ms total) -48: -48: [----------] 13 tests from StringTableTest -48: [ RUN ] StringTableTest.AddSingleEntry -48: [ OK ] StringTableTest.AddSingleEntry (13 ms) -48: [ RUN ] StringTableTest.CanAccessWithAt -48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) -48: [ RUN ] StringTableTest.CanAccessWithBracket -48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) -48: [ RUN ] StringTableTest.ThrowsOutOfRange -48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) -48: [ RUN ] StringTableTest.StringCompareIsCorrect -48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) -48: [ RUN ] StringTableTest.AddTwoDistinctEntries -48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) -48: [ RUN ] StringTableTest.TryToAddDuplicates -48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) -48: [ RUN ] StringTableTest.AddLargeNumberOfEntries -48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) -48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable -48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) -48: [ RUN ] StringTableTest.CanWriteToBuffer -48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) -48: [ RUN ] StringTableTest.Roundtrip -48: [ OK ] StringTableTest.Roundtrip (0 ms) -48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices -48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) -48: [ RUN ] StringTableTest.CanCopyToLegacyTable -48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) -48: [----------] 13 tests from StringTableTest (15 ms total) -48: -48: [----------] 6 tests from LegacySymtabTest -48: [ RUN ] LegacySymtabTest.EmptyOnOpen -48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) -48: [ RUN ] LegacySymtabTest.AddSingleEntry -48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) -48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries -48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) -48: [ RUN ] LegacySymtabTest.TryToAddDuplicates -48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) -48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries -48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) -48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable -48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) -48: [----------] 6 tests from LegacySymtabTest (0 ms total) -48: -48: [----------] 5 tests from TopSortTest -48: [ RUN ] TopSortTest.WorksOnEmptyIdef -48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) -48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction -48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) -48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) -48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) -48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) -48: [----------] 5 tests from TopSortTest (0 ms total) -48: -48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (113 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) -48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (125 ms total) -48: -48: [----------] Global test environment tear-down -48: [==========] 153 tests from 10 test suites ran. (157 ms total) -48: [ PASSED ] 153 tests. -48: -48: YOU HAVE 1 DISABLED TEST -48: -48/92 Test #48: TopologyTest .............................. Passed 0.18 sec -test 49 - Start 49: PullTest - -49: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/PullTest.xml" -49: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/pulling/tests -49: Test timeout computed to be: 30 -49: [==========] Running 10 tests from 1 test suite. -49: [----------] Global test environment set-up. -49: [----------] 10 tests from PullTest -49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox -49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox -49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox -49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox -49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox -49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) -49: [ RUN ] PullTest.TransformationCoordSimple -49: [ OK ] PullTest.TransformationCoordSimple (0 ms) -49: [ RUN ] PullTest.TransformationCoordAdvanced -49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) -49: [ RUN ] PullTest.TransformationCoordTime -49: [ OK ] PullTest.TransformationCoordTime (0 ms) -49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed -49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) -49: [ RUN ] PullTest.TransformationCoordDummyExpression -49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) -49: [----------] 10 tests from PullTest (0 ms total) -49: -49: [----------] Global test environment tear-down -49: [==========] 10 tests from 1 test suite ran. (0 ms total) -49: [ PASSED ] 10 tests. -49/92 Test #49: PullTest .................................. Passed 0.01 sec -test 50 - Start 50: SimdUnitTests - -50: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/SimdUnitTests.xml" -50: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/simd/tests -50: Test timeout computed to be: 30 -50: [==========] Running 288 tests from 22 test suites. -50: [----------] Global test environment set-up. -50: [----------] 9 tests from SimdBootstrapTest -50: [ RUN ] SimdBootstrapTest.loadStore -50: [ OK ] SimdBootstrapTest.loadStore (0 ms) -50: [ RUN ] SimdBootstrapTest.loadU -50: [ OK ] SimdBootstrapTest.loadU (0 ms) -50: [ RUN ] SimdBootstrapTest.storeU -50: [ OK ] SimdBootstrapTest.storeU (0 ms) -50: [ RUN ] SimdBootstrapTest.loadStoreI -50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) -50: [ RUN ] SimdBootstrapTest.loadUI -50: [ OK ] SimdBootstrapTest.loadUI (0 ms) -50: [ RUN ] SimdBootstrapTest.storeUI -50: [ OK ] SimdBootstrapTest.storeUI (0 ms) -50: [ RUN ] SimdBootstrapTest.simd4LoadStore -50: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) -50: [ RUN ] SimdBootstrapTest.simd4LoadU -50: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) -50: [ RUN ] SimdBootstrapTest.simd4StoreU -50: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) -50: [----------] 9 tests from SimdBootstrapTest (0 ms total) -50: -50: [----------] 41 tests from SimdScalarTest -50: [ RUN ] SimdScalarTest.load -50: [ OK ] SimdScalarTest.load (0 ms) -50: [ RUN ] SimdScalarTest.loadU -50: [ OK ] SimdScalarTest.loadU (0 ms) -50: [ RUN ] SimdScalarTest.store -50: [ OK ] SimdScalarTest.store (0 ms) -50: [ RUN ] SimdScalarTest.storeU -50: [ OK ] SimdScalarTest.storeU (0 ms) -50: [ RUN ] SimdScalarTest.setZero -50: [ OK ] SimdScalarTest.setZero (0 ms) -50: [ RUN ] SimdScalarTest.andNot -50: [ OK ] SimdScalarTest.andNot (0 ms) -50: [ RUN ] SimdScalarTest.fma -50: [ OK ] SimdScalarTest.fma (0 ms) -50: [ RUN ] SimdScalarTest.fms -50: [ OK ] SimdScalarTest.fms (0 ms) -50: [ RUN ] SimdScalarTest.fnma -50: [ OK ] SimdScalarTest.fnma (0 ms) -50: [ RUN ] SimdScalarTest.fnms -50: [ OK ] SimdScalarTest.fnms (0 ms) -50: [ RUN ] SimdScalarTest.maskAdd -50: [ OK ] SimdScalarTest.maskAdd (0 ms) -50: [ RUN ] SimdScalarTest.maskzMul -50: [ OK ] SimdScalarTest.maskzMul (0 ms) -50: [ RUN ] SimdScalarTest.maskzFma -50: [ OK ] SimdScalarTest.maskzFma (0 ms) -50: [ RUN ] SimdScalarTest.abs -50: [ OK ] SimdScalarTest.abs (0 ms) -50: [ RUN ] SimdScalarTest.max -50: [ OK ] SimdScalarTest.max (0 ms) -50: [ RUN ] SimdScalarTest.min -50: [ OK ] SimdScalarTest.min (0 ms) -50: [ RUN ] SimdScalarTest.round -50: [ OK ] SimdScalarTest.round (0 ms) -50: [ RUN ] SimdScalarTest.trunc -50: [ OK ] SimdScalarTest.trunc (0 ms) -50: [ RUN ] SimdScalarTest.reduce -50: [ OK ] SimdScalarTest.reduce (0 ms) -50: [ RUN ] SimdScalarTest.testBits -50: [ OK ] SimdScalarTest.testBits (0 ms) -50: [ RUN ] SimdScalarTest.anyTrue -50: [ OK ] SimdScalarTest.anyTrue (0 ms) -50: [ RUN ] SimdScalarTest.selectByMask -50: [ OK ] SimdScalarTest.selectByMask (0 ms) -50: [ RUN ] SimdScalarTest.selectByNotMask -50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) -50: [ RUN ] SimdScalarTest.blend -50: [ OK ] SimdScalarTest.blend (0 ms) -50: [ RUN ] SimdScalarTest.cvtR2I -50: [ OK ] SimdScalarTest.cvtR2I (0 ms) -50: [ RUN ] SimdScalarTest.cvttR2I -50: [ OK ] SimdScalarTest.cvttR2I (0 ms) -50: [ RUN ] SimdScalarTest.cvtI2R -50: [ OK ] SimdScalarTest.cvtI2R (0 ms) -50: [ RUN ] SimdScalarTest.cvtF2D -50: [ OK ] SimdScalarTest.cvtF2D (0 ms) -50: [ RUN ] SimdScalarTest.cvtD2D -50: [ OK ] SimdScalarTest.cvtD2D (0 ms) -50: [ RUN ] SimdScalarTest.loadI -50: [ OK ] SimdScalarTest.loadI (0 ms) -50: [ RUN ] SimdScalarTest.loadUI -50: [ OK ] SimdScalarTest.loadUI (0 ms) -50: [ RUN ] SimdScalarTest.storeI -50: [ OK ] SimdScalarTest.storeI (0 ms) -50: [ RUN ] SimdScalarTest.storeUI -50: [ OK ] SimdScalarTest.storeUI (0 ms) -50: [ RUN ] SimdScalarTest.andNotI -50: [ OK ] SimdScalarTest.andNotI (0 ms) -50: [ RUN ] SimdScalarTest.testBitsI -50: [ OK ] SimdScalarTest.testBitsI (0 ms) -50: [ RUN ] SimdScalarTest.selectByMaskI -50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) -50: [ RUN ] SimdScalarTest.selectByNotMaskI -50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) -50: [ RUN ] SimdScalarTest.blendI -50: [ OK ] SimdScalarTest.blendI (0 ms) -50: [ RUN ] SimdScalarTest.cvtB2IB -50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) -50: [ RUN ] SimdScalarTest.cvtIB2B -50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) -50: [ RUN ] SimdScalarTest.expandScalarsToTriplets -50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) -50: [----------] 41 tests from SimdScalarTest (0 ms total) -50: -50: [----------] 8 tests from SimdScalarUtilTest -50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU -50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU -50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU -50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum -50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) -50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) -50: -50: [----------] 37 tests from SimdScalarMathTest -50: [ RUN ] SimdScalarMathTest.copysign -50: [ OK ] SimdScalarMathTest.copysign (0 ms) -50: [ RUN ] SimdScalarMathTest.invsqrtPair -50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) -50: [ RUN ] SimdScalarMathTest.inv -50: [ OK ] SimdScalarMathTest.inv (0 ms) -50: [ RUN ] SimdScalarMathTest.maskzInvsqrt -50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) -50: [ RUN ] SimdScalarMathTest.log -50: [ OK ] SimdScalarMathTest.log (0 ms) -50: [ RUN ] SimdScalarMathTest.exp2 -50: [ OK ] SimdScalarMathTest.exp2 (0 ms) -50: [ RUN ] SimdScalarMathTest.exp -50: [ OK ] SimdScalarMathTest.exp (0 ms) -50: [ RUN ] SimdScalarMathTest.erf -50: [ OK ] SimdScalarMathTest.erf (0 ms) -50: [ RUN ] SimdScalarMathTest.erfc -50: [ OK ] SimdScalarMathTest.erfc (0 ms) -50: [ RUN ] SimdScalarMathTest.sincos -50: [ OK ] SimdScalarMathTest.sincos (0 ms) -50: [ RUN ] SimdScalarMathTest.sin -50: [ OK ] SimdScalarMathTest.sin (0 ms) -50: [ RUN ] SimdScalarMathTest.cos -50: [ OK ] SimdScalarMathTest.cos (0 ms) -50: [ RUN ] SimdScalarMathTest.tan -50: [ OK ] SimdScalarMathTest.tan (0 ms) -50: [ RUN ] SimdScalarMathTest.asin -50: [ OK ] SimdScalarMathTest.asin (0 ms) -50: [ RUN ] SimdScalarMathTest.acos -50: [ OK ] SimdScalarMathTest.acos (0 ms) -50: [ RUN ] SimdScalarMathTest.atan -50: [ OK ] SimdScalarMathTest.atan (0 ms) -50: [ RUN ] SimdScalarMathTest.atan2 -50: [ OK ] SimdScalarMathTest.atan2 (0 ms) -50: [ RUN ] SimdScalarMathTest.pmeForceCorrection -50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) -50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection -50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) -50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy -50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.invSingleAccuracy -50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy -50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.logSingleAccuracy -50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy -50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.expSingleAccuracy -50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy -50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy -50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy -50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy -50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy -50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy -50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy -50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy -50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy -50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy -50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy -50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy -50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -50: [----------] 37 tests from SimdScalarMathTest (0 ms total) -50: -50: [----------] 1 test from SimdTest -50: [ RUN ] SimdTest.GmxAligned -50: [ OK ] SimdTest.GmxAligned (0 ms) -50: [----------] 1 test from SimdTest (0 ms total) -50: -50: [----------] 42 tests from SimdFloatingpointTest -50: [ RUN ] SimdFloatingpointTest.setZero -50: [ OK ] SimdFloatingpointTest.setZero (0 ms) -50: [ RUN ] SimdFloatingpointTest.set -50: [ OK ] SimdFloatingpointTest.set (0 ms) -50: [ RUN ] SimdFloatingpointTest.add -50: [ OK ] SimdFloatingpointTest.add (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskAdd -50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) -50: [ RUN ] SimdFloatingpointTest.sub -50: [ OK ] SimdFloatingpointTest.sub (0 ms) -50: [ RUN ] SimdFloatingpointTest.mul -50: [ OK ] SimdFloatingpointTest.mul (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzMul -50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) -50: [ RUN ] SimdFloatingpointTest.fma -50: [ OK ] SimdFloatingpointTest.fma (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzFma -50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) -50: [ RUN ] SimdFloatingpointTest.fms -50: [ OK ] SimdFloatingpointTest.fms (0 ms) -50: [ RUN ] SimdFloatingpointTest.fnma -50: [ OK ] SimdFloatingpointTest.fnma (0 ms) -50: [ RUN ] SimdFloatingpointTest.fnms -50: [ OK ] SimdFloatingpointTest.fnms (0 ms) -50: [ RUN ] SimdFloatingpointTest.abs -50: [ OK ] SimdFloatingpointTest.abs (0 ms) -50: [ RUN ] SimdFloatingpointTest.neg -50: [ OK ] SimdFloatingpointTest.neg (0 ms) -50: [ RUN ] SimdFloatingpointTest.and -50: [ OK ] SimdFloatingpointTest.and (0 ms) -50: [ RUN ] SimdFloatingpointTest.or -50: [ OK ] SimdFloatingpointTest.or (0 ms) -50: [ RUN ] SimdFloatingpointTest.xor -50: [ OK ] SimdFloatingpointTest.xor (0 ms) -50: [ RUN ] SimdFloatingpointTest.andNot -50: [ OK ] SimdFloatingpointTest.andNot (0 ms) -50: [ RUN ] SimdFloatingpointTest.max -50: [ OK ] SimdFloatingpointTest.max (0 ms) -50: [ RUN ] SimdFloatingpointTest.min -50: [ OK ] SimdFloatingpointTest.min (0 ms) -50: [ RUN ] SimdFloatingpointTest.round -50: [ OK ] SimdFloatingpointTest.round (0 ms) -50: [ RUN ] SimdFloatingpointTest.roundMode -50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) -50: [ RUN ] SimdFloatingpointTest.trunc -50: [ OK ] SimdFloatingpointTest.trunc (0 ms) -50: [ RUN ] SimdFloatingpointTest.frexp -50: [ OK ] SimdFloatingpointTest.frexp (0 ms) -50: [ RUN ] SimdFloatingpointTest.ldexp -50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) -50: [ RUN ] SimdFloatingpointTest.rsqrt -50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzRsqrt -50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) -50: [ RUN ] SimdFloatingpointTest.rcp -50: [ OK ] SimdFloatingpointTest.rcp (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzRcp -50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask -50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) -50: [ RUN ] SimdFloatingpointTest.selectByNotMask -50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpNe -50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpLe -50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpLt -50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) -50: [ RUN ] SimdFloatingpointTest.testBits -50: [ OK ] SimdFloatingpointTest.testBits (0 ms) -50: [ RUN ] SimdFloatingpointTest.andB -50: [ OK ] SimdFloatingpointTest.andB (0 ms) -50: [ RUN ] SimdFloatingpointTest.orB -50: [ OK ] SimdFloatingpointTest.orB (0 ms) -50: [ RUN ] SimdFloatingpointTest.anyTrueB -50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) -50: [ RUN ] SimdFloatingpointTest.blend -50: [ OK ] SimdFloatingpointTest.blend (0 ms) -50: [ RUN ] SimdFloatingpointTest.reduce -50: [ OK ] SimdFloatingpointTest.reduce (0 ms) -50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double -50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) -50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float -50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) -50: [----------] 42 tests from SimdFloatingpointTest (0 ms total) -50: -50: [----------] 16 tests from SimdFloatingpointUtilTest -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets -50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum -50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 -50: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN -50: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset -50: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) -50: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) -50: -50: [----------] 23 tests from SimdIntegerTest -50: [ RUN ] SimdIntegerTest.setZero -50: [ OK ] SimdIntegerTest.setZero (0 ms) -50: [ RUN ] SimdIntegerTest.set -50: [ OK ] SimdIntegerTest.set (0 ms) -50: [ RUN ] SimdIntegerTest.add -50: [ OK ] SimdIntegerTest.add (0 ms) -50: [ RUN ] SimdIntegerTest.sub -50: [ OK ] SimdIntegerTest.sub (0 ms) -50: [ RUN ] SimdIntegerTest.mul -50: [ OK ] SimdIntegerTest.mul (0 ms) -50: [ RUN ] SimdIntegerTest.and -50: [ OK ] SimdIntegerTest.and (0 ms) -50: [ RUN ] SimdIntegerTest.andNot -50: [ OK ] SimdIntegerTest.andNot (0 ms) -50: [ RUN ] SimdIntegerTest.or -50: [ OK ] SimdIntegerTest.or (0 ms) -50: [ RUN ] SimdIntegerTest.xor -50: [ OK ] SimdIntegerTest.xor (0 ms) -50: [ RUN ] SimdIntegerTest.extract -50: [ OK ] SimdIntegerTest.extract (0 ms) -50: [ RUN ] SimdIntegerTest.cvtR2I -50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) -50: [ RUN ] SimdIntegerTest.cvttR2I -50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) -50: [ RUN ] SimdIntegerTest.cvtI2R -50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) -50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask -50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) -50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask -50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) -50: [ RUN ] SimdIntegerTest.cmpLt -50: [ OK ] SimdIntegerTest.cmpLt (0 ms) -50: [ RUN ] SimdIntegerTest.testBits -50: [ OK ] SimdIntegerTest.testBits (0 ms) -50: [ RUN ] SimdIntegerTest.andB -50: [ OK ] SimdIntegerTest.andB (0 ms) -50: [ RUN ] SimdIntegerTest.orB -50: [ OK ] SimdIntegerTest.orB (0 ms) -50: [ RUN ] SimdIntegerTest.anyTrue -50: [ OK ] SimdIntegerTest.anyTrue (0 ms) -50: [ RUN ] SimdIntegerTest.blend -50: [ OK ] SimdIntegerTest.blend (0 ms) -50: [ RUN ] SimdIntegerTest.cvtB2IB -50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) -50: [ RUN ] SimdIntegerTest.cvtIB2B -50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) -50: [----------] 23 tests from SimdIntegerTest (0 ms total) -50: -50: [----------] 56 tests from SimdMathTest -50: [ RUN ] SimdMathTest.generateTestPointsFloat -50: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) -50: [ RUN ] SimdMathTest.copysign -50: [ OK ] SimdMathTest.copysign (0 ms) -50: [ RUN ] SimdMathTest.invsqrt -50: [ OK ] SimdMathTest.invsqrt (0 ms) -50: [ RUN ] SimdMathTest.maskzInvsqrt -50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) -50: [ RUN ] SimdMathTest.invsqrtPair -50: [ OK ] SimdMathTest.invsqrtPair (0 ms) -50: [ RUN ] SimdMathTest.sqrt -50: [ OK ] SimdMathTest.sqrt (0 ms) -50: [ RUN ] SimdMathTest.sqrtUnsafe -50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) -50: [ RUN ] SimdMathTest.inv -50: [ OK ] SimdMathTest.inv (2 ms) -50: [ RUN ] SimdMathTest.maskzInv -50: [ OK ] SimdMathTest.maskzInv (0 ms) -50: [ RUN ] SimdMathTest.cbrt -50: [ OK ] SimdMathTest.cbrt (0 ms) -50: [ RUN ] SimdMathTest.invcbrt -50: [ OK ] SimdMathTest.invcbrt (1 ms) -50: [ RUN ] SimdMathTest.log2 -50: [ OK ] SimdMathTest.log2 (0 ms) -50: [ RUN ] SimdMathTest.log -50: [ OK ] SimdMathTest.log (0 ms) -50: [ RUN ] SimdMathTest.exp2 -50: [ OK ] SimdMathTest.exp2 (1 ms) -50: [ RUN ] SimdMathTest.exp2Unsafe -50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) -50: [ RUN ] SimdMathTest.exp -50: [ OK ] SimdMathTest.exp (1 ms) -50: [ RUN ] SimdMathTest.expUnsafe -50: [ OK ] SimdMathTest.expUnsafe (0 ms) -50: [ RUN ] SimdMathTest.pow -50: [ OK ] SimdMathTest.pow (0 ms) -50: [ RUN ] SimdMathTest.powUnsafe -50: [ OK ] SimdMathTest.powUnsafe (0 ms) -50: [ RUN ] SimdMathTest.erf -50: [ OK ] SimdMathTest.erf (0 ms) -50: [ RUN ] SimdMathTest.erfc -50: [ OK ] SimdMathTest.erfc (0 ms) -50: [ RUN ] SimdMathTest.sin -50: [ OK ] SimdMathTest.sin (0 ms) -50: [ RUN ] SimdMathTest.cos -50: [ OK ] SimdMathTest.cos (0 ms) -50: [ RUN ] SimdMathTest.tan -50: [ OK ] SimdMathTest.tan (0 ms) -50: [ RUN ] SimdMathTest.asin -50: [ OK ] SimdMathTest.asin (0 ms) -50: [ RUN ] SimdMathTest.acos -50: [ OK ] SimdMathTest.acos (0 ms) -50: [ RUN ] SimdMathTest.atan -50: [ OK ] SimdMathTest.atan (0 ms) -50: [ RUN ] SimdMathTest.atan2 -50: [ OK ] SimdMathTest.atan2 (0 ms) -50: [ RUN ] SimdMathTest.pmeForceCorrection -50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) -50: [ RUN ] SimdMathTest.pmePotentialCorrection -50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) -50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy -50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy -50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sqrtSingleAccuracy -50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.invSingleAccuracy -50: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) -50: [ RUN ] SimdMathTest.cbrtSingleAccuracy -50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy -50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.log2SingleAccuracy -50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.logSingleAccuracy -50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.exp2SingleAccuracy -50: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe -50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.expSingleAccuracy -50: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.powSingleAccuracy -50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.erfSingleAccuracy -50: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.erfcSingleAccuracy -50: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sinSingleAccuracy -50: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.cosSingleAccuracy -50: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.tanSingleAccuracy -50: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.asinSingleAccuracy -50: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.acosSingleAccuracy -50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.atanSingleAccuracy -50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.atan2SingleAccuracy -50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy -50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy -50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -50: [----------] 56 tests from SimdMathTest (30 ms total) -50: -50: [----------] 1 test from EmptyArrayRefTest -50: [ RUN ] EmptyArrayRefTest.IsEmpty -50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -50: [----------] 1 test from EmptyArrayRefTest (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) -50: -50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefReadWriteTest/0.Assignment -50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) -50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) -50: -50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefReadWriteTest/1.Assignment -50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) -50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) -50: -50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefArithmeticTest/0.Basic -50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) -50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) -50: -50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefArithmeticTest/1.Basic -50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) -50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) -50: -50: [----------] 3 tests from SimdVectorOperationsTest -50: [ RUN ] SimdVectorOperationsTest.iprod -50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) -50: [ RUN ] SimdVectorOperationsTest.norm2 -50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) -50: [ RUN ] SimdVectorOperationsTest.cprod -50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) -50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) -50: -50: [----------] 32 tests from Simd4FloatingpointTest -50: [ RUN ] Simd4FloatingpointTest.setZero -50: [ OK ] Simd4FloatingpointTest.setZero (0 ms) -50: [ RUN ] Simd4FloatingpointTest.set -50: [ OK ] Simd4FloatingpointTest.set (0 ms) -50: [ RUN ] Simd4FloatingpointTest.add -50: [ OK ] Simd4FloatingpointTest.add (0 ms) -50: [ RUN ] Simd4FloatingpointTest.sub -50: [ OK ] Simd4FloatingpointTest.sub (0 ms) -50: [ RUN ] Simd4FloatingpointTest.mul -50: [ OK ] Simd4FloatingpointTest.mul (0 ms) -50: [ RUN ] Simd4FloatingpointTest.fma -50: [ OK ] Simd4FloatingpointTest.fma (0 ms) -50: [ RUN ] Simd4FloatingpointTest.fms -50: [ OK ] Simd4FloatingpointTest.fms (0 ms) -50: [ RUN ] Simd4FloatingpointTest.fnma -50: [ OK ] Simd4FloatingpointTest.fnma (0 ms) -50: [ RUN ] Simd4FloatingpointTest.fnms -50: [ OK ] Simd4FloatingpointTest.fnms (0 ms) -50: [ RUN ] Simd4FloatingpointTest.abs -50: [ OK ] Simd4FloatingpointTest.abs (0 ms) -50: [ RUN ] Simd4FloatingpointTest.neg -50: [ OK ] Simd4FloatingpointTest.neg (0 ms) -50: [ RUN ] Simd4FloatingpointTest.and -50: [ OK ] Simd4FloatingpointTest.and (0 ms) -50: [ RUN ] Simd4FloatingpointTest.or -50: [ OK ] Simd4FloatingpointTest.or (0 ms) -50: [ RUN ] Simd4FloatingpointTest.xor -50: [ OK ] Simd4FloatingpointTest.xor (0 ms) -50: [ RUN ] Simd4FloatingpointTest.andNot -50: [ OK ] Simd4FloatingpointTest.andNot (0 ms) -50: [ RUN ] Simd4FloatingpointTest.max -50: [ OK ] Simd4FloatingpointTest.max (0 ms) -50: [ RUN ] Simd4FloatingpointTest.min -50: [ OK ] Simd4FloatingpointTest.min (0 ms) -50: [ RUN ] Simd4FloatingpointTest.round -50: [ OK ] Simd4FloatingpointTest.round (0 ms) -50: [ RUN ] Simd4FloatingpointTest.trunc -50: [ OK ] Simd4FloatingpointTest.trunc (0 ms) -50: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR -50: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) -50: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask -50: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) -50: [ RUN ] Simd4FloatingpointTest.selectByNotMask -50: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) -50: [ RUN ] Simd4FloatingpointTest.cmpNe -50: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) -50: [ RUN ] Simd4FloatingpointTest.cmpLe -50: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) -50: [ RUN ] Simd4FloatingpointTest.cmpLt -50: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) -50: [ RUN ] Simd4FloatingpointTest.andB -50: [ OK ] Simd4FloatingpointTest.andB (0 ms) -50: [ RUN ] Simd4FloatingpointTest.orB -50: [ OK ] Simd4FloatingpointTest.orB (0 ms) -50: [ RUN ] Simd4FloatingpointTest.anyTrue -50: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) -50: [ RUN ] Simd4FloatingpointTest.blend -50: [ OK ] Simd4FloatingpointTest.blend (0 ms) -50: [ RUN ] Simd4FloatingpointTest.reduce -50: [ OK ] Simd4FloatingpointTest.reduce (0 ms) -50: [ RUN ] Simd4FloatingpointTest.dotProduct -50: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) -50: [ RUN ] Simd4FloatingpointTest.transpose -50: [ OK ] Simd4FloatingpointTest.transpose (0 ms) -50: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) -50: -50: [----------] 2 tests from Simd4MathTest -50: [ RUN ] Simd4MathTest.invsqrt -50: [ OK ] Simd4MathTest.invsqrt (0 ms) -50: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy -50: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) -50: [----------] 2 tests from Simd4MathTest (0 ms total) -50: -50: [----------] 1 test from Simd4VectorOperationsTest -50: [ RUN ] Simd4VectorOperationsTest.norm2 -50: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) -50: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) -50: -50: [----------] Global test environment tear-down -50: [==========] 288 tests from 22 test suites ran. (31 ms total) -50: [ PASSED ] 288 tests. -50/92 Test #50: SimdUnitTests ............................. Passed 0.05 sec -test 51 - Start 51: CompatibilityHelpersTests - -51: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" -51: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/compat/tests -51: Test timeout computed to be: 30 -51: [==========] Running 9 tests from 6 test suites. -51: [----------] Global test environment set-up. -51: [----------] 4 tests from TemplateMPTest -51: [ RUN ] TemplateMPTest.MpWithIndexInt -51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexIntBad -51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexBool -51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexEnum -51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) -51: [----------] 4 tests from TemplateMPTest (0 ms total) -51: -51: [----------] 1 test from NotNullConstruction -51: [ RUN ] NotNullConstruction.Works -51: [ OK ] NotNullConstruction.Works (0 ms) -51: [----------] 1 test from NotNullConstruction (0 ms total) -51: -51: [----------] 1 test from NotNullCasting -51: [ RUN ] NotNullCasting.Works -51: [ OK ] NotNullCasting.Works (0 ms) -51: [----------] 1 test from NotNullCasting (0 ms total) -51: -51: [----------] 1 test from NotNullAssignment -51: [ RUN ] NotNullAssignment.Works -51: [ OK ] NotNullAssignment.Works (0 ms) -51: [----------] 1 test from NotNullAssignment (0 ms total) -51: -51: [----------] 1 test from MakeNotNull -51: [ RUN ] MakeNotNull.Works -51: [ OK ] MakeNotNull.Works (0 ms) -51: [----------] 1 test from MakeNotNull (0 ms total) -51: -51: [----------] 1 test from NotNull -51: [ RUN ] NotNull.WorksInContainers -51: [ OK ] NotNull.WorksInContainers (0 ms) -51: [----------] 1 test from NotNull (0 ms total) -51: -51: [----------] Global test environment tear-down -51: [==========] 9 tests from 6 test suites ran. (0 ms total) -51: [ PASSED ] 9 tests. -51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.01 sec -test 52 - Start 52: GmxAnaTest - -52: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxAnaTest.xml" -52: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxana/tests -52: Test timeout computed to be: 600 -52: [==========] Running 31 tests from 4 test suites. -52: [----------] Global test environment set-up. -52: [----------] 7 tests from Entropy -52: [ RUN ] Entropy.Schlitter_300_NoLinear -52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) -52: [ RUN ] Entropy.Schlitter_300_Linear -52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear -52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear -52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_200_Linear -52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) -52: [ RUN ] Entropy.EntropyCompare_200_Linear -52: [ OK ] Entropy.EntropyCompare_200_Linear (5 ms) -52: [ RUN ] Entropy.EntropyCompare_300_Linear -52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) -52: [----------] 7 tests from Entropy (5 ms total) -52: -52: [----------] 2 tests from GmxChiTest -52: [ RUN ] GmxChiTest.gmxchiWorksWithAll -52: Analyzing from residue 1 to residue 11 -52: 10 residues with dihedrals found -52: 46 dihedrals found -52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -52: j after resetting (nr. active dihedrals) = 46 -52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg -52: Now calculating transitions... -52: Total number of transitions: 0 -52: Now printing out transitions and OPs... -52: Now printing out rotamer occupancies... -52: Now calculating Chi product trajectories... -52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg -52: [ OK ] GmxChiTest.gmxchiWorksWithAll (831 ms) -52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN -52: Analyzing from residue 2 to residue 6 -52: 5 residues with dihedrals found -52: 23 dihedrals found -52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -52: j after resetting (nr. active dihedrals) = 23 -52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg -52: Now calculating transitions... -52: Total number of transitions: 0 -52: Now printing out transitions and OPs... -52: Now printing out rotamer occupancies... -52: Now calculating Chi product trajectories... -52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg -52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (298 ms) -52: [----------] 2 tests from GmxChiTest (1209 ms total) -52: -52: [----------] 10 tests from MindistTest -52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (324 ms) -52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 2: 'atom3' -52: Selected 3: 'atoms12' -52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) -52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) -52: [ RUN ] MindistTest.mindistPicksUpContacts -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) -52: [ RUN ] MindistTest.ngWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.ngWorks (0 ms) -52: [ RUN ] MindistTest.groupWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 3: 'atoms12' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.groupWorks (194 ms) -52: [ RUN ] MindistTest.maxDistWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 2: 'atom3' -52: Selected 3: 'atoms12' -52: [ OK ] MindistTest.maxDistWorks (80 ms) -52: [ RUN ] MindistTest.noPbcWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.noPbcWorks (0 ms) -52: [ RUN ] MindistTest.resPerTimeWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 3: 'atoms12' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.resPerTimeWorks (175 ms) -52: [ RUN ] MindistTest.matrixWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 5: 'atoms123' -52: Special case: making distance matrix between all atoms in group atoms123 -52: [ OK ] MindistTest.matrixWorks (1 ms) -52: [----------] 10 tests from MindistTest (780 ms total) -52: -52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: trr version: GMX_trn_file (single precision) -52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (261 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (80 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (2 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (2 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -52: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (2 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (2 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (2 ms) -52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (362 ms total) -52: -52: [----------] Global test environment tear-down -52: [==========] 31 tests from 4 test suites ran. (2358 ms total) -52: [ PASSED ] 31 tests. -52/92 Test #52: GmxAnaTest ................................ Passed 2.38 sec -test 53 - Start 53: GmxPreprocessTests - -53: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/GmxPreprocessTests.xml" -53: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests -53: Test timeout computed to be: 1920 -53: [==========] Running 260 tests from 16 test suites. -53: [----------] Global test environment set-up. -53: [----------] 1 test from ConvertInteractionsTest -53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks -53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) -53: [----------] 1 test from ConvertInteractionsTest (0 ms total) -53: -53: [----------] 4 tests from GenconfTest -53: [ RUN ] GenconfTest.nbox_Works -53: [ OK ] GenconfTest.nbox_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_norenumber_Works -53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_dist_Works -53: [ OK ] GenconfTest.nbox_dist_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_rot_Works -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: [ OK ] GenconfTest.nbox_rot_Works (0 ms) -53: [----------] 4 tests from GenconfTest (2 ms total) -53: -53: [----------] 2 tests from GenionTest -53: [ RUN ] GenionTest.HighConcentrationIonPlacement -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -53: buffer. The cluster pair list does have a buffering effect, but choosing -53: a larger rlist might be necessary for good energy conservation. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -53: < 0 -53: -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: Generating 1-4 interactions: fudge = 0.5 -53: Number of degrees of freedom in T-Coupling group rest is 1308.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: You are using a plain Coulomb cut-off, which might produce artifacts. -53: You might want to consider using PME electrostatics. -53: -53: -53: -53: There were 4 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -53: Group 0 ( System) has 653 elements -53: Group 1 ( Water) has 648 elements -53: Group 2 ( SOL) has 648 elements -53: Group 3 ( non-Water) has 5 elements -53: Group 4 ( Other) has 5 elements -53: Group 5 ( METH) has 5 elements -53: Select a group: Number of (3-atomic) solvent molecules: 216 -53: Using random seed 1997. -53: Replacing solvent molecule 56 (atom 168) with NA -53: Replacing solvent molecule 120 (atom 360) with NA -53: Replacing solvent molecule 182 (atom 546) with NA -53: Replacing solvent molecule 71 (atom 213) with NA -53: Replacing solvent molecule 189 (atom 567) with CL -53: Replacing solvent molecule 54 (atom 162) with CL -53: Replacing solvent molecule 155 (atom 465) with CL -53: Replacing solvent molecule 99 (atom 297) with CL -53: -53: Setting the LD random seed to 284659663 -53: -53: Generated 331705 of the 331705 non-bonded parameter combinations -53: -53: Generated 331705 of the 331705 1-4 parameter combinations -53: -53: Excluding 2 bonded neighbours molecule type 'SOL' -53: -53: Excluding 3 bonded neighbours molecule type 'methane' -53: -53: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -53: Analysing residue names: -53: There are: 216 Water residues -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: This run will generate roughly 0 Mb of data -53: Will try to add 4 NA ions and 4 CL ions. -53: Select a continuous group of solvent molecules -53: Selected 1: 'Water' -53: [ OK ] GenionTest.HighConcentrationIonPlacement (213 ms) -53: [ RUN ] GenionTest.NoIonPlacement -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -53: buffer. The cluster pair list does have a buffering effect, but choosing -53: a larger rlist might be necessary for good energy conservation. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -53: < 0 -53: -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: Generating 1-4 interactions: fudge = 0.5 -53: Number of degrees of freedom in T-Coupling group rest is 1308.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: You are using a plain Coulomb cut-off, which might produce artifacts. -53: You might want to consider using PME electrostatics. -53: -53: -53: -53: There were 4 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -53: No ions to add, will just copy input configuration. -53: Setting the LD random seed to -709895681 -53: -53: Generated 331705 of the 331705 non-bonded parameter combinations -53: -53: Generated 331705 of the 331705 1-4 parameter combinations -53: -53: Excluding 2 bonded neighbours molecule type 'SOL' -53: -53: Excluding 3 bonded neighbours molecule type 'methane' -53: -53: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -53: Analysing residue names: -53: There are: 216 Water residues -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GenionTest.NoIonPlacement (201 ms) -53: [----------] 2 tests from GenionTest (414 ms total) -53: -53: [----------] 1 test from GenRestrTest -53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated -53: -53: Reading structure file -53: Group 0 ( System) has 156 elements -53: Group 1 ( Protein) has 156 elements -53: Group 2 ( Protein-H) has 75 elements -53: Group 3 ( C-alpha) has 10 elements -53: Group 4 ( Backbone) has 30 elements -53: Group 5 ( MainChain) has 40 elements -53: Group 6 ( MainChain+Cb) has 49 elements -53: Group 7 ( MainChain+H) has 52 elements -53: Group 8 ( SideChain) has 104 elements -53: Group 9 ( SideChain-H) has 35 elements -53: Select a group: Select group to position restrain -53: Selected 3: 'C-alpha' -53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) -53: [----------] 1 test from GenRestrTest (1 ms total) -53: -53: [----------] 9 tests from PreprocessingAtomTypesTest -53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate -53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid -53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks -53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks -53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry -53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound -53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound -53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber -53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber -53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) -53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) -53: -53: [----------] 10 tests from PreprocessingBondAtomTypeTest -53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate -53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid -53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks -53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks -53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry -53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType -53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound -53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound -53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber -53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber -53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) -53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) -53: -53: [----------] 3 tests from GromppDirectiveTest -53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives.top, line 59]: -53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 9.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -53: Setting the LD random seed to -1075499174 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -956327061 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (28 ms) -53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives.top, line 59]: -53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have -53: coefficients that do not sum to zero. This does not affect the simulation -53: and can be ignored, unless you are comparing potential energy values with -53: other force field ports and/or MD software. -53: First such dihedral in molecule A, involving atoms 0 2 1 3 -53: -53: -53: NOTE 2 [file directives.top, line 59]: -53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 9.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 3 NOTEs -53: Setting the LD random seed to -44401826 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -134234500 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (8 ms) -53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy -53: Setting the LD random seed to -35738147 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -138630226 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (7 ms) -53: [----------] 3 tests from GromppDirectiveTest (44 ms total) -53: -53: [----------] 6 tests from InsertMoleculesTest -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 8 atoms)! -53: -53: Added 1 molecules (out of 1 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro -53: -53: Output configuration contains 8 atoms in 4 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 success (now 6 atoms)! -53: Try 4 success (now 8 atoms)! -53: Try 5 success (now 10 atoms)! -53: -53: Added 5 molecules (out of 5 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro -53: -53: Output configuration contains 10 atoms in 10 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (31 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 success (now 6 atoms)! -53: Try 4 success (now 8 atoms)! -53: Try 5 success (now 10 atoms)! -53: -53: Added 5 molecules (out of 5 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro -53: -53: Output configuration contains 10 atoms in 10 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (1 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 8 atoms)! -53: Try 2 success (now 10 atoms)! -53: -53: Added 2 molecules (out of 2 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro -53: -53: Output configuration contains 10 atoms in 4 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 650 atoms)! -53: Try 2 success (now 652 atoms)! -53: Try 3 success (now 654 atoms)! -53: Try 4 success (now 656 atoms)! -53: -53: Added 4 molecules (out of 4 requested) -53: Replaced 8 residues (24 atoms) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro -53: -53: Output configuration contains 632 atoms in 212 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Read 4 positions from file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat -53: -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) -53: Try 13 success (now 6 atoms)! -53: -53: Added 3 molecules (out of 4 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro -53: -53: Output configuration contains 6 atoms in 3 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (7 ms) -53: [----------] 6 tests from InsertMoleculesTest (44 ms total) -53: -53: [----------] 3 tests from MassRepartitioning -53: [ RUN ] MassRepartitioning.ValidCaseWorks -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) -53: [ RUN ] MassRepartitioning.UnboundGivesWarning -53: -53: WARNING 1 [file unknown]: -53: The are 1 atoms that have a mass below the mass repartitioning limit but -53: are not bound. These masses cannot be repartitioned. -53: -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) -53: [ RUN ] MassRepartitioning.LightPartnerGivesError -53: -53: ERROR 1 [file unknown]: -53: Light atoms are bound to at least one atom that has a too low mass for -53: repartitioning -53: -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) -53: [----------] 3 tests from MassRepartitioning (0 ms total) -53: -53: [----------] 35 tests from GetIrTest -53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines -53: Ignoring obsolete mdp entry 'title' -53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) -53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals -53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (4 ms) -53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) -53: [ RUN ] GetIrTest.RejectsValueWithoutKey -53: [ OK ] GetIrTest.RejectsValueWithoutKey (4 ms) -53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue -53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (3 ms) -53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) -53: [ RUN ] GetIrTest.AcceptsEmptyLines -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstenergy -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: Setting nstcalcenergy (100) equal to nstenergy (5) -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstpcouple -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -53: Pressure coupling incorrect number of values (I need exactly 1) -53: -53: -53: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -53: Pressure coupling incorrect number of values (I need exactly 1) -53: -53: -53: ERROR 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: With multiple time stepping, nstpcouple should be a multiple of -53: mts-factor -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: -53: ERROR 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: The Berendsen barostat does not generate any strictly correct ensemble, -53: and should not be used for new production simulations (in our opinion). -53: We recommend using the C-rescale barostat instead. -53: -53: -53: ERROR 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: compressibility must be > 0 when using pressure coupling Berendsen -53: -53: -53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstdhdl -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: Setting nstcalcenergy (100) equal to nstdhdl (5) -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: -53: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: Lambda state must be set, either with init-lambda-state or with -53: init-lambda -53: -53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) -53: [ RUN ] GetIrTest.MtsCheckSDNotSupported -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -53: Multiple time stepping is only supported with integrator md -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricField -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricField (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) -53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys -53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) -53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) -53: [ RUN ] GetIrTest.RejectsImplicitSolventYes -53: [ OK ] GetIrTest.RejectsImplicitSolventYes (3 ms) -53: [ RUN ] GetIrTest.AcceptsMimic -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsMimic (97 ms) -53: [ RUN ] GetIrTest.AcceptsTransformationCoord -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: -53: pull-coord2 has a non-zero force constant and is also referenced in -53: pull-coord1-expression. Make sure that this is intended. In most use -53: cases, the pull coordinates referenced by a transformation coordinate -53: should have their force constant set to zero. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) -53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: -53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) -53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: -53: pull-coord2 can not use pull-coord1 in the transformation since this is a -53: constraint -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) -53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: -53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry -53: 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) -53: [ RUN ] GetIrTest.MissingTransformationCoordExpression -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: -53: pull-coord1-expression not set for pull coordinate of geometry -53: 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: -53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, -53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of -53: in total 100001 steps. This is not compatible with using soft-core -53: potentials. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -53: won't change anymore after step 100000 until the end of the simulation -53: after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -53: won't change anymore after step 100000 until the end of the simulation -53: after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: -53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda -53: components won't change anymore after step 100000 until the end of the -53: simulation after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda -53: components won't change anymore after step 100000 until the end of the -53: simulation after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [----------] 35 tests from GetIrTest (159 ms total) -53: -53: [----------] 6 tests from SolvateTest -53: [ RUN ] SolvateTest.cs_box_Works -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 1x1x1 boxes -53: Solvent box contains 270 atoms in 90 residues -53: Removed 129 solvent atoms due to solvent-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 47 residues -53: Generated solvent containing 141 atoms in 47 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro -53: -53: Output configuration contains 141 atoms in 47 residues -53: Volume : 1.331 (nm^3) -53: Density : 1056.36 (g/l) -53: Number of solvent molecules: 47 -53: -53: [ OK ] SolvateTest.cs_box_Works (2 ms) -53: [ RUN ] SolvateTest.cs_cp_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 886 residues -53: Generated solvent containing 2658 atoms in 886 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro -53: -53: Output configuration contains 2664 atoms in 888 residues -53: Volume : 27.2709 (nm^3) -53: Density : 974.777 (g/l) -53: Number of solvent molecules: 886 -53: -53: [ OK ] SolvateTest.cs_cp_Works (94 ms) -53: [ RUN ] SolvateTest.cs_cp_p_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 886 residues -53: Generated solvent containing 2658 atoms in 886 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro -53: -53: Output configuration contains 2664 atoms in 888 residues -53: Volume : 27.2709 (nm^3) -53: Density : 974.777 (g/l) -53: Number of solvent molecules: 886 -53: -53: Processing topology -53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) -53: [ OK ] SolvateTest.cs_cp_p_Works (144 ms) -53: [ RUN ] SolvateTest.shell_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 1902 solvent atoms more than 1.000000 nm from solute. -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 252 residues -53: Generated solvent containing 756 atoms in 252 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro -53: -53: Output configuration contains 762 atoms in 254 residues -53: Volume : 27.2709 (nm^3) -53: Density : 279.3 (g/l) -53: Number of solvent molecules: 252 -53: -53: [ OK ] SolvateTest.shell_Works (8 ms) -53: [ RUN ] SolvateTest.update_Topology_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 3x3x3 boxes -53: Solvent box contains 14952 atoms in 4984 residues -53: Removed 2787 solvent atoms due to solvent-solvent overlap -53: Removed 30 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 2 different molecule types: -53: HOH ( 3 atoms): 1876 residues -53: SOL ( 3 atoms): 2169 residues -53: Generated solvent containing 0 atoms in 0 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro -53: -53: Output configuration contains 12141 atoms in 4047 residues -53: Volume : 125 (nm^3) -53: Density : 968.963 (g/l) -53: Number of solvent molecules: 4045 -53: -53: Processing topology -53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -53: [ OK ] SolvateTest.update_Topology_Works (68 ms) -53: [ RUN ] SolvateTest.cs_pdb_big_box_Works -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 1218 atoms in 406 residues -53: Removed 555 solvent atoms due to solvent-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 221 residues -53: Generated solvent containing 663 atoms in 221 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro -53: -53: Output configuration contains 663 atoms in 221 residues -53: Volume : 8 (nm^3) -53: Density : 826.409 (g/l) -53: Number of solvent molecules: 221 -53: -53: [ OK ] SolvateTest.cs_pdb_big_box_Works (5 ms) -53: [----------] 6 tests from SolvateTest (324 ms total) -53: -53: [----------] 1 test from TopDirTests -53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize -53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) -53: [----------] 1 test from TopDirTests (0 ms total) -53: -53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) -53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) -53: -53: [----------] 45 tests from SinglePeptideFragments/EditconfTest -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (6 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (7 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (12 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (4 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (6 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 -53: -53: Select a group for output: -53: Group 0 ( two_residues) has 23 elements -53: There is one group in the index -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (9 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : 0.212 1.187 3.527 (nm) -53: new center : 4.028 2.819 3.723 (nm) -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.42 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.42 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.42 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (4 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: shift : -0.814 1.104 2.657 (nm) -53: new center : 3.002 2.736 2.852 (nm) -53: new box vectors : 6.004 5.472 5.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 187.40 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.28 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (15 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.28 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.28 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (12 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (5 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) -53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 -53: Note that major changes are planned in future for editconf, to improve usability and utility. -53: Read 252 atoms -53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -53: No velocities found -53: system size : 2.004 1.472 1.704 (nm) -53: center : 3.816 1.632 0.195 (nm) -53: box vectors : 8.056 5.637 7.445 (nm) -53: box angles : 90.00 90.00 90.00 (degrees) -53: box volume : 338.10 (nm^3) -53: new center : 3.816 1.632 0.195 (nm) -53: new box vectors : 5.004 4.472 4.704 (nm) -53: new box angles : 90.00 90.00 90.00 (degrees) -53: new box volume : 105.27 (nm^3) -53: -53: WARNING: No boxtype specified - distance condition applied in each dimension. -53: If the molecule rotates the actual distance will be smaller. You might want -53: to use a cubic box instead, or why not try a dodecahedron today? -53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) -53: [----------] 45 tests from SinglePeptideFragments/EditconfTest (145 ms total) -53: -53: [----------] 16 tests from CorrectVelocity/MaxwellTest -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (9 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (2 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) -53: [----------] 16 tests from CorrectVelocity/MaxwellTest (21 ms total) -53: -53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 -53: Setting the LD random seed to -4465187 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (8 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 -53: Setting the LD random seed to -814023941 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (6 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to 1794897725 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -805410582 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (3 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -1073774792 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 330480949 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (4 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -33686041 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -288374797 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (4 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -314573345 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 2029975214 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (3 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 -53: Setting the LD random seed to -135741449 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (6 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 -53: Setting the LD random seed to 1979694702 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 1941961215 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (6 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 -53: Setting the LD random seed to 2109717455 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (77 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 -53: Setting the LD random seed to -631246865 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 2147481375 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (77 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 -53: Setting the LD random seed to -1078218755 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -4260747 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (177 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 -53: Setting the LD random seed to -1114669123 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -141656162 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (12 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 -53: Setting the LD random seed to -1212940305 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -234897929 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (6 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 -53: Setting the LD random seed to -4153 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -335546645 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (48 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 -53: Setting the LD random seed to 1539168735 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 2013265783 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (38 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 -53: Setting the LD random seed to -1074790681 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1367411714 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (34 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -26428485 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -18088451 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (13 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -100938305 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1140957713 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (23 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 -53: Setting the LD random seed to 2011164095 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (11 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 -53: Setting the LD random seed to 2012985341 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 452918770 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (15 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 -53: Setting the LD random seed to -1183056402 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (10 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -100958226 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -470254853 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (7 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 -53: Setting the LD random seed to -18902337 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (7 ms) -53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (607 ms total) -53: -53: [----------] Global test environment tear-down -53: [==========] 260 tests from 16 test suites ran. (1769 ms total) -53: [ PASSED ] 220 tests. -53: [ SKIPPED ] 40 tests, listed below: -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -53/92 Test #53: GmxPreprocessTests ........................ Passed 1.79 sec -test 54 - Start 54: Pdb2gmx1Test - -54: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" -54: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests -54: Test timeout computed to be: 1920 -54: [==========] Running 30 tests from 1 test suite. -54: [----------] Global test environment set-up. -54: [----------] 30 tests from Oplsaa/Pdb2gmxTest -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (55 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (30 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (191 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (15 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (33 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (42 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge -0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) -54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1072 ms total) -54: -54: [----------] Global test environment tear-down -54: [==========] 30 tests from 1 test suite ran. (1072 ms total) -54: [ PASSED ] 30 tests. -54/92 Test #54: Pdb2gmx1Test .............................. Passed 1.09 sec -test 55 - Start 55: Pdb2gmx2Test - -55: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" -55: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests -55: Test timeout computed to be: 1920 -55: [==========] Running 40 tests from 2 test suites. -55: [----------] Global test environment set-up. -55: [----------] 20 tests from G43a1/Pdb2gmxTest -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (47 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 37 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 37 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (27 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 53 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 51 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 36 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 36 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 33 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 31 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 146 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 137 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (286 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (140 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 37 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 37 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 53 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 51 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 36 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 36 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 33 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 31 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 146 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 137 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) -55: [----------] 20 tests from G43a1/Pdb2gmxTest (979 ms total) -55: -55: [----------] 20 tests from G53a6/Pdb2gmxTest -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (32 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (31 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 39 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 39 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (28 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 57 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 55 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 38 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 38 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (55 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 35 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 33 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 150 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 141 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (35 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (25 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 39 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 39 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 57 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 55 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 38 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 38 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (31 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 35 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 33 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 150 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 141 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) -55: [----------] 20 tests from G53a6/Pdb2gmxTest (689 ms total) -55: -55: [----------] Global test environment tear-down -55: [==========] 40 tests from 2 test suites ran. (1669 ms total) -55: [ PASSED ] 40 tests. -55/92 Test #55: Pdb2gmx2Test .............................. Passed 1.68 sec -test 56 - Start 56: Pdb2gmx3Test - -56: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" -56: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/gmxpreprocess/tests -56: Test timeout computed to be: 1920 -56: [==========] Running 39 tests from 6 test suites. -56: [----------] Global test environment set-up. -56: [----------] 10 tests from Amber/Pdb2gmxTest -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 653 pairs -56: Before cleaning: 691 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 255, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 691 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.132 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (40 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 748 pairs -56: Before cleaning: 788 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 291, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 788 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.366 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 676 pairs -56: Before cleaning: 727 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 262, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 727 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.124 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 603 pairs -56: Before cleaning: 634 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 233, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 634 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.888 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 2499 pairs -56: Before cleaning: 2631 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 952, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2631 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.576 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (66 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 691 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 255, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 691 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.132 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 788 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 291, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 788 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.366 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 727 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 262, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 727 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.124 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (28 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 634 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 233, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 634 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.888 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2631 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 952, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2631 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.576 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (64 ms) -56: [----------] 10 tests from Amber/Pdb2gmxTest (347 ms total) -56: -56: [----------] 1 test from AmberTip4p/Pdb2gmxTest -56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... -56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 2 4 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (4 atoms, 2 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 2 residues with 8 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 4, now 4 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 2 angles -56: 0 pairs, 4 bonds and 0 virtual sites -56: -56: Total mass 36.032 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. -56: -56: The Amber99sb-ildn force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (19 ms) -56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (19 ms total) -56: -56: [----------] 12 tests from Charmm/Pdb2gmxTest -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 663 dihedrals, 48 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.115 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 778 dihedrals, 49 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.361 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 696 dihedrals, 39 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.130 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 618 dihedrals, 38 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.885 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 56 cmap torsion pairs -56: -56: There are 2524 dihedrals, 149 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.566 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (48 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 39 pairs -56: Before cleaning: 39 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -56: Read 'GLU', 9 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -56: -56: chain #res #atoms -56: -56: 1 'X' 1 9 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'X' (9 atoms, 1 residues) -56: -56: Identified residue GLU1 as a starting terminus. -56: -56: Identified residue GLU1 as a ending terminus. -56: Start terminus GLU-1: NH3+ -56: End terminus GLU-1: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 1 residues with 18 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 17, now 17 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 39 dihedrals, 2 impropers, 30 angles -56: 39 pairs, 17 bonds and 0 virtual sites -56: -56: Total mass 146.123 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (11 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 663 dihedrals, 48 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.115 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 778 dihedrals, 49 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.361 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 696 dihedrals, 39 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.130 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (32 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 618 dihedrals, 38 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.885 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 56 cmap torsion pairs -56: -56: There are 2524 dihedrals, 149 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.566 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 8 virtual sites -56: Added 2 dummy masses -56: Added 3 new constraints -56: Before cleaning: 39 pairs -56: Before cleaning: 39 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -56: Read 'GLU', 9 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -56: -56: chain #res #atoms -56: -56: 1 'X' 1 9 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'X' (9 atoms, 1 residues) -56: -56: Identified residue GLU1 as a starting terminus. -56: -56: Identified residue GLU1 as a ending terminus. -56: Start terminus GLU-1: NH3+ -56: End terminus GLU-1: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 1 residues with 18 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 17, now 17 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 39 dihedrals, 2 impropers, 30 angles -56: 39 pairs, 17 bonds and 9 virtual sites -56: -56: Total mass 146.123 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (12 ms) -56: [----------] 12 tests from Charmm/Pdb2gmxTest (312 ms total) -56: -56: [----------] 8 tests from ChainSep/Pdb2gmxTest -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 651 pairs -56: Before cleaning: 661 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: Start terminus PHE-6: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 258 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 258, now 258 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 10 cmap torsion pairs -56: -56: There are 661 dihedrals, 46 impropers, 463 angles -56: 648 pairs, 258 bonds and 0 virtual sites -56: -56: Total mass 1882.146 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (38 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 123 pairs -56: Before cleaning: 123 dihedrals -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 10 donors and 7 acceptors were found. -56: There are 7 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS8 -56: NE223 -56: MET12 SD55 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 317 pairs -56: Before cleaning: 322 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 4 28 -56: -56: 2 'B' 7 58 -56: -56: 3 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (28 atoms, 4 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 51 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 50, now 50 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 123 dihedrals, 9 impropers, 88 angles -56: 123 pairs, 50 bonds and 0 virtual sites -56: -56: Total mass 434.421 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (58 atoms, 7 residues) -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus PHE-6: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 7 residues with 124 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 125, now 125 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 5 cmap torsion pairs -56: -56: There are 322 dihedrals, 19 impropers, 227 angles -56: 314 pairs, 125 bonds and 0 virtual sites -56: -56: Total mass 846.083 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 51 atoms 4 residues -56: -56: Including chain 2 in system: 124 atoms 7 residues -56: -56: Including chain 3 in system: 83 atoms 5 residues -56: -56: Now there are 258 atoms and 16 residues -56: -56: Total mass in system 1882.146 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (26 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 651 pairs -56: Before cleaning: 661 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ILE-9: COO- -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 258 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 258, now 258 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 10 cmap torsion pairs -56: -56: There are 661 dihedrals, 46 impropers, 463 angles -56: 648 pairs, 258 bonds and 0 virtual sites -56: -56: Total mass 1882.146 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 10 donors and 12 acceptors were found. -56: There are 13 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 -56: SG9 -56: HIS8 NE251 1.055 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 288 pairs -56: Before cleaning: 293 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 152 pairs -56: Before cleaning: 152 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 8 61 -56: -56: 2 'B' 3 25 -56: -56: 3 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (61 atoms, 8 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ILE-9: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 8 residues with 114 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 115, now 115 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6 cmap torsion pairs -56: -56: There are 293 dihedrals, 23 impropers, 203 angles -56: 285 pairs, 115 bonds and 0 virtual sites -56: -56: Total mass 888.952 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (25 atoms, 3 residues) -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 61 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 60, now 60 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 152 dihedrals, 5 impropers, 112 angles -56: 152 pairs, 60 bonds and 0 virtual sites -56: -56: Total mass 391.552 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 114 atoms 8 residues -56: -56: Including chain 2 in system: 61 atoms 3 residues -56: -56: Including chain 3 in system: 83 atoms 5 residues -56: -56: Now there are 258 atoms and 16 residues -56: -56: Total mass in system 1882.146 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 650 pairs -56: Before cleaning: 660 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Merged chains into joint molecule definitions at 3 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: Start terminus PHE-6: NH3+ -56: End terminus ILE-9: COO- -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 261 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 260, now 260 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 8 cmap torsion pairs -56: -56: There are 660 dihedrals, 45 impropers, 466 angles -56: 647 pairs, 260 bonds and 0 virtual sites -56: -56: Total mass 1900.162 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (25 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 123 pairs -56: Before cleaning: 123 dihedrals -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 6 donors and 4 acceptors were found. -56: There are 3 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 164 pairs -56: Before cleaning: 169 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 152 pairs -56: Before cleaning: 152 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 4 28 -56: -56: 2 'B' 4 33 -56: -56: 3 'B' 3 25 -56: -56: 4 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (28 atoms, 4 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 51 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 50, now 50 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 123 dihedrals, 9 impropers, 88 angles -56: 123 pairs, 50 bonds and 0 virtual sites -56: -56: Total mass 434.421 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (33 atoms, 4 residues) -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: Start terminus PHE-6: NH3+ -56: End terminus ILE-9: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 66 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 67, now 67 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 169 dihedrals, 13 impropers, 118 angles -56: 161 pairs, 67 bonds and 0 virtual sites -56: -56: Total mass 472.547 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'B' (25 atoms, 3 residues) -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 61 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 60, now 60 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 152 dihedrals, 5 impropers, 112 angles -56: 152 pairs, 60 bonds and 0 virtual sites -56: -56: Total mass 391.552 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 4 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 51 atoms 4 residues -56: -56: Including chain 2 in system: 66 atoms 4 residues -56: -56: Including chain 3 in system: 61 atoms 3 residues -56: -56: Including chain 4 in system: 83 atoms 5 residues -56: -56: Now there are 261 atoms and 16 residues -56: -56: Total mass in system 1900.162 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (24 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 652 pairs -56: Before cleaning: 662 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: Merged chains into joint molecule definitions at 1 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 256, now 256 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 12 cmap torsion pairs -56: -56: There are 662 dihedrals, 47 impropers, 460 angles -56: 649 pairs, 256 bonds and 0 virtual sites -56: -56: Total mass 1864.131 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (25 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 14 donors and 15 acceptors were found. -56: There are 20 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 441 pairs -56: Before cleaning: 446 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 11 86 -56: -56: 2 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (86 atoms, 11 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 11 residues with 172 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 173, now 173 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 9 cmap torsion pairs -56: -56: There are 446 dihedrals, 29 impropers, 312 angles -56: 438 pairs, 173 bonds and 0 virtual sites -56: -56: Total mass 1262.488 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 172 atoms 11 residues -56: -56: Including chain 2 in system: 83 atoms 5 residues -56: -56: Now there are 255 atoms and 16 residues -56: -56: Total mass in system 1864.131 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (25 ms) -56: [----------] 8 tests from ChainSep/Pdb2gmxTest (207 ms total) -56: -56: [----------] 4 tests from ChainChanges/Pdb2gmxTest -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (21 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (15 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (16 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (20 ms) -56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (73 ms total) -56: -56: [----------] 4 tests from Cyclic/Pdb2gmxTest -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: WARNING: all CONECT records are ignored -56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 6040 pairs -56: Before cleaning: 6605 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 6040 pairs -56: Before cleaning: 6605 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: Moved all the water blocks to the end -56: -56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms -56: -56: chain #res #atoms -56: -56: 1 'P' 71 1527 -56: -56: 2 'Q' 71 1527 -56: -56: 3 'Q' 7 7 -56: -56: 4 ' ' 10 10 (only water) -56: -56: 5 ' ' 16 16 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'P' (1527 atoms, 71 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 71 residues with 2297 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 2481, now 2481 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6605 dihedrals, 183 impropers, 4434 angles -56: 5827 pairs, 2481 bonds and 0 virtual sites -56: -56: Total mass 22984.514 a.m.u. -56: -56: Total charge -71.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'Q' (1527 atoms, 71 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 71 residues with 2297 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 2481, now 2481 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6605 dihedrals, 183 impropers, 4434 angles -56: 5827 pairs, 2481 bonds and 0 virtual sites -56: -56: Total mass 22984.514 a.m.u. -56: -56: Total charge -71.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'Q' (7 atoms, 7 residues) -56: -56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -56: -56: Disabling further notes about ions. -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 7 residues with 7 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: No bonds -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 0 angles -56: 0 pairs, 0 bonds and 0 virtual sites -56: -56: Total mass 170.135 a.m.u. -56: -56: Total charge 14.000 e -56: -56: Writing topology -56: -56: Processing chain 4 (10 atoms, 10 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 10 residues with 30 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 30, now 30 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 30 angles -56: 0 pairs, 30 bonds and 0 virtual sites -56: -56: Total mass 180.154 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Processing chain 5 (16 atoms, 16 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 48 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 48, now 48 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 48 angles -56: 0 pairs, 48 bonds and 0 virtual sites -56: -56: Total mass 288.246 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Including chain 1 in system: 2297 atoms 71 residues -56: -56: Including chain 2 in system: 2297 atoms 71 residues -56: -56: Including chain 3 in system: 7 atoms 7 residues -56: -56: Including chain 4 in system: 30 atoms 10 residues -56: -56: Including chain 5 in system: 48 atoms 16 residues -56: -56: Now there are 4679 atoms and 175 residues -56: -56: Total mass in system 46607.562 a.m.u. -56: -56: Total charge in system -128.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (185 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2325 pairs -56: Before cleaning: 2325 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -56: Read 'CARNOCYCLIN-A', 413 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 60 413 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (413 atoms, 60 residues) -56: -56: Identified residue LEU1 as a starting terminus. -56: -56: Identified residue LEU60 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 60 residues with 878 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 880, now 880 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 60 cmap torsion pairs -56: -56: There are 2325 dihedrals, 137 impropers, 1614 angles -56: 2319 pairs, 880 bonds and 0 virtual sites -56: -56: Total mass 5866.087 a.m.u. -56: -56: Total charge 4.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (45 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: WARNING: all CONECT records are ignored -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 12080 pairs -56: Before cleaning: 13210 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Moved all the water blocks to the end -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms -56: -56: chain #res #atoms -56: -56: 1 'P' 149 3061 -56: -56: 2 ' ' 10 10 (only water) -56: -56: 3 ' ' 16 16 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'P' (3061 atoms, 149 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -56: -56: Disabling further notes about ions. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 149 residues with 4601 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 4962, now 4962 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 13210 dihedrals, 366 impropers, 8868 angles -56: 11654 pairs, 4962 bonds and 0 virtual sites -56: -56: Total mass 46139.162 a.m.u. -56: -56: Total charge -128.000 e -56: -56: Writing topology -56: -56: Processing chain 2 (10 atoms, 10 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 10 residues with 30 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 30, now 30 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 30 angles -56: 0 pairs, 30 bonds and 0 virtual sites -56: -56: Total mass 180.154 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Processing chain 3 (16 atoms, 16 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 48 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 48, now 48 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 48 angles -56: 0 pairs, 48 bonds and 0 virtual sites -56: -56: Total mass 288.246 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Including chain 1 in system: 4601 atoms 149 residues -56: -56: Including chain 2 in system: 30 atoms 10 residues -56: -56: Including chain 3 in system: 48 atoms 16 residues -56: -56: Now there are 4679 atoms and 175 residues -56: -56: Total mass in system 46607.562 a.m.u. -56: -56: Total charge in system -128.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (340 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2325 pairs -56: Before cleaning: 2325 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -56: Read 'CARNOCYCLIN-A', 413 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 60 413 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (413 atoms, 60 residues) -56: -56: Identified residue LEU1 as a starting terminus. -56: -56: Identified residue LEU60 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 60 residues with 878 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 880, now 880 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 60 cmap torsion pairs -56: -56: There are 2325 dihedrals, 137 impropers, 1614 angles -56: 2319 pairs, 880 bonds and 0 virtual sites -56: -56: Total mass 5866.087 a.m.u. -56: -56: Total charge 4.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (139 ms) -56: [----------] 4 tests from Cyclic/Pdb2gmxTest (711 ms total) -56: -56: [----------] Global test environment tear-down -56: [==========] 39 tests from 6 test suites ran. (1670 ms total) -56: [ PASSED ] 39 tests. -56/92 Test #56: Pdb2gmx3Test .............................. Passed 1.68 sec -test 57 - Start 57: CorrelationsTest - -57: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/CorrelationsTest.xml" -57: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/correlationfunctions/tests -57: Test timeout computed to be: 30 -57: [==========] Running 21 tests from 3 test suites. -57: [----------] Global test environment set-up. -57: [----------] 10 tests from AutocorrTest -57: [ RUN ] AutocorrTest.EacNormal -57: [ OK ] AutocorrTest.EacNormal (38 ms) -57: [ RUN ] AutocorrTest.EacNoNormalize -57: [ OK ] AutocorrTest.EacNoNormalize (22 ms) -57: [ RUN ] AutocorrTest.EacCos -57: [ OK ] AutocorrTest.EacCos (47 ms) -57: [ RUN ] AutocorrTest.EacVector -57: [ OK ] AutocorrTest.EacVector (68 ms) -57: [ RUN ] AutocorrTest.EacRcross -57: [ OK ] AutocorrTest.EacRcross (1 ms) -57: [ RUN ] AutocorrTest.EacP0 -57: [ OK ] AutocorrTest.EacP0 (76 ms) -57: [ RUN ] AutocorrTest.EacP1 -57: [ OK ] AutocorrTest.EacP1 (71 ms) -57: [ RUN ] AutocorrTest.EacP2 -57: [ OK ] AutocorrTest.EacP2 (143 ms) -57: [ RUN ] AutocorrTest.EacP3 -57: [ OK ] AutocorrTest.EacP3 (2 ms) -57: [ RUN ] AutocorrTest.EacP4 -57: [ OK ] AutocorrTest.EacP4 (71 ms) -57: [----------] 10 tests from AutocorrTest (544 ms total) -57: -57: [----------] 10 tests from ExpfitTest -57: [ RUN ] ExpfitTest.EffnEXP1 -57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) -57: [ RUN ] ExpfitTest.EffnEXP2 -57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) -57: [ RUN ] ExpfitTest.EffnEXPEXP -57: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) -57: [ RUN ] ExpfitTest.EffnEXP5 -57: [ OK ] ExpfitTest.EffnEXP5 (2 ms) -57: [ RUN ] ExpfitTest.EffnEXP7 -57: [ OK ] ExpfitTest.EffnEXP7 (1 ms) -57: [ RUN ] ExpfitTest.EffnEXP9 -57: [ OK ] ExpfitTest.EffnEXP9 (8 ms) -57: [ RUN ] ExpfitTest.EffnERF -57: [ OK ] ExpfitTest.EffnERF (1 ms) -57: [ RUN ] ExpfitTest.EffnERREST -57: [ OK ] ExpfitTest.EffnERREST (1 ms) -57: [ RUN ] ExpfitTest.EffnVAC -57: [ OK ] ExpfitTest.EffnVAC (3 ms) -57: [ RUN ] ExpfitTest.EffnPRES -57: [ OK ] ExpfitTest.EffnPRES (9 ms) -57: [----------] 10 tests from ExpfitTest (30 ms total) -57: -57: [----------] 1 test from ManyAutocorrelationTest -57: [ RUN ] ManyAutocorrelationTest.Empty -57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) -57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) -57: -57: [----------] Global test environment tear-down -57: [==========] 21 tests from 3 test suites ran. (579 ms total) -57: [ PASSED ] 21 tests. -57/92 Test #57: CorrelationsTest .......................... Passed 0.59 sec -test 58 - Start 58: AnalysisDataUnitTests - -58: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" -58: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/analysisdata/tests -58: Test timeout computed to be: 30 -58: [==========] Running 69 tests from 14 test suites. -58: [----------] Global test environment set-up. -58: [----------] 3 tests from AnalysisDataInitializationTest -58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization -58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) -58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules -58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) -58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules -58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) -58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData -58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData -58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData -58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData -58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/3 (2 ms total) -58: -58: [----------] 4 tests from AnalysisArrayDataTest -58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly -58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisArrayDataTest.StorageWorks -58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) -58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis -58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) -58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount -58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) -58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) -58: -58: [----------] 6 tests from AverageModuleTest -58: [ RUN ] AverageModuleTest.BasicTest -58: [ OK ] AverageModuleTest.BasicTest (0 ms) -58: [ RUN ] AverageModuleTest.HandlesMultipointData -58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) -58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets -58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging -58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) -58: [ RUN ] AverageModuleTest.CanCustomizeXAxis -58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) -58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis -58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) -58: [----------] 6 tests from AverageModuleTest (2 ms total) -58: -58: [----------] 2 tests from FrameAverageModuleTest -58: [ RUN ] FrameAverageModuleTest.BasicTest -58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) -58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets -58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 2 tests from FrameAverageModuleTest (0 ms total) -58: -58: [----------] 7 tests from AnalysisHistogramSettingsTest -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) -58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) -58: -58: [----------] 2 tests from SimpleHistogramModuleTest -58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly -58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) -58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll -58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -58: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) -58: -58: [----------] 3 tests from WeightedHistogramModuleTest -58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly -58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (6 ms) -58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll -58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets -58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 3 tests from WeightedHistogramModuleTest (7 ms total) -58: -58: [----------] 3 tests from BinAverageModuleTest -58: [ RUN ] BinAverageModuleTest.ComputesCorrectly -58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) -58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll -58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (3 ms) -58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets -58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 3 tests from BinAverageModuleTest (4 ms total) -58: -58: [----------] 4 tests from AbstractAverageHistogramTest -58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly -58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram -58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth -58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins -58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) -58: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) -58: -58: [----------] 3 tests from LifetimeModuleTest -58: [ RUN ] LifetimeModuleTest.BasicTest -58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) -58: [ RUN ] LifetimeModuleTest.CumulativeTest -58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) -58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets -58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) -58: [----------] 3 tests from LifetimeModuleTest (2 ms total) -58: -58: [----------] Global test environment tear-down -58: [==========] 69 tests from 14 test suites ran. (30 ms total) -58: [ PASSED ] 69 tests. -58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.04 sec -test 59 - Start 59: CoordinateIOTests - -59: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/CoordinateIOTests.xml" -59: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/coordinateio/tests -59: Test timeout computed to be: 30 -59: [==========] Running 67 tests from 20 test suites. -59: [----------] Global test environment set-up. -59: [----------] 1 test from OutputSelectorDeathTest -59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (9 ms) -59: [----------] 1 test from OutputSelectorDeathTest (9 ms total) -59: -59: [----------] 5 tests from TrajectoryFrameWriterTest -59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (2 ms) -59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks -59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) -59: [----------] 5 tests from TrajectoryFrameWriterTest (5 ms total) -59: -59: [----------] 5 tests from OutputAdapterContainer -59: [ RUN ] OutputAdapterContainer.MakeEmpty -59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) -59: [ RUN ] OutputAdapterContainer.AddAdapter -59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.RejectBadAdapter -59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter -59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters -59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) -59: [----------] 5 tests from OutputAdapterContainer (0 ms total) -59: -59: [----------] 3 tests from RegisterFrameConverterTest -59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks -59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) -59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks -59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) -59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees -59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) -59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) -59: -59: [----------] 5 tests from FlagTest -59: [ RUN ] FlagTest.CanSetSimpleFlag -59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) -59: [ RUN ] FlagTest.CanAddNewBox -59: [ OK ] FlagTest.CanAddNewBox (0 ms) -59: [ RUN ] FlagTest.SetsImplicitPrecisionChange -59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) -59: [ RUN ] FlagTest.SetsImplicitStartTimeChange -59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) -59: [ RUN ] FlagTest.SetsImplicitTimeStepChange -59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) -59: [----------] 5 tests from FlagTest (0 ms total) -59: -59: [----------] 5 tests from SetAtomsTest -59: [ RUN ] SetAtomsTest.RemovesExistingAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) -59: [ RUN ] SetAtomsTest.AddsNewAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) -59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) -59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) -59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) -59: [----------] 5 tests from SetAtomsTest (6 ms total) -59: -59: [----------] 2 tests from SetBothTimeTest -59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks -59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) -59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks -59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) -59: [----------] 2 tests from SetBothTimeTest (0 ms total) -59: -59: [----------] 2 tests from SetStartTimeTest -59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart -59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) -59: [ RUN ] SetStartTimeTest.WorksWithZeroStart -59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) -59: [----------] 2 tests from SetStartTimeTest (0 ms total) -59: -59: [----------] 1 test from SetTimeStepTest -59: [ RUN ] SetTimeStepTest.SetTimeStepWorks -59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) -59: [----------] 1 test from SetTimeStepTest (0 ms total) -59: -59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) -59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (8 ms total) -59: -59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) -59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (3 ms total) -59: -59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) -59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) -59: -59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) -59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (10 ms total) -59: -59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) -59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (4 ms total) -59: -59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) -59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) -59: -59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles -59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) -59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) -59: -59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) -59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) -59: -59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles -59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) -59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) -59: -59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) -59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) -59: -59: [----------] 4 tests from ModuleSupported/NoOptionalOutput -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) -59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) -59: -59: [----------] Global test environment tear-down -59: [==========] 67 tests from 20 test suites ran. (61 ms total) -59: [ PASSED ] 67 tests. -59/92 Test #59: CoordinateIOTests ......................... Passed 0.07 sec -test 60 - Start 60: TrajectoryAnalysisUnitTests - -60: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" -60: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests -60: Test timeout computed to be: 1920 -60: [==========] Running 393 tests from 21 test suites. -60: [----------] Global test environment set-up. -60: [----------] 11 tests from AngleModuleTest -60: [ RUN ] AngleModuleTest.ComputesSimpleAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesSimpleAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesDihedrals -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles -60: Reading frames from gro file 'Test system for different angles', 33 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (15 ms) -60: [ RUN ] AngleModuleTest.ComputesMultipleAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) -60: [ RUN ] AngleModuleTest.HandlesDynamicSelections -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) -60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) -60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (4 ms) -60: [----------] 11 tests from AngleModuleTest (33 ms total) -60: -60: [----------] 5 tests from ClustsizeTest -60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -60: There is one group in the index -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 24 -60: cmid: 2, cmax: 4, max_size: 6 -60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (2 ms) -60: [ RUN ] ClustsizeTest.NoMolShortCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -60: There is one group in the index -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 24 -60: cmid: 1, cmax: 6, max_size: 6 -60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) -60: [ RUN ] ClustsizeTest.MolDefaultCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 2, cmax: 4, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (21 ms) -60: [ RUN ] ClustsizeTest.MolShortCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 1, cmax: 6, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (4 ms) -60: [ RUN ] ClustsizeTest.MolCSize -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 2, cmax: 4, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolCSize (10 ms) -60: [----------] 5 tests from ClustsizeTest (39 ms total) -60: -60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory -60: Reading frames from gro file 'Test system', 8 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (1 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset -60: Reading frames from gro file 'Test system', 8 atoms. -60: Reading frame 0 time 0.000 -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) -60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) -60: -60: [----------] 4 tests from ConvertTrjModuleTest -60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (19 ms) -60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (17 ms) -60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (6 ms) -60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) -60: [----------] 4 tests from ConvertTrjModuleTest (44 ms total) -60: -60: [----------] 6 tests from DistanceModuleTest -60: [ RUN ] DistanceModuleTest.ComputesDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2: -60: Number of samples: 5 -60: Average distance: 1.43246 nm -60: Standard deviation: 0.96700 nm -60: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) -60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2: -60: Number of samples: 5 -60: Average distance: 1.43246 nm -60: Standard deviation: 0.96700 nm -60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: -60: Number of samples: 4 -60: Average distance: 1.81066 nm -60: Standard deviation: 0.79289 nm -60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) -60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2 and res_cog x < 2.8: -60: Number of samples: 3 -60: Average distance: 1.72076 nm -60: Standard deviation: 1.24839 nm -60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: Contacts: -60: Number of samples: 2 -60: Average distance: 1.00000 nm -60: Standard deviation: 0.00000 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: SuccessiveContacts: -60: Number of samples: 2 -60: Average distance: 1.00000 nm -60: Standard deviation: 0.00000 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: ManyContacts: -60: Number of samples: 10 -60: Average distance: 1.82913 nm -60: Standard deviation: 0.78478 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) -60: [----------] 6 tests from DistanceModuleTest (16 ms total) -60: -60: [----------] 2 tests from ExtractClusterModuleTest -60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms -60: trr version: GMX_trn_file (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -60: Analyzed 26 frames, last time 0.050 -60: There are 8 clusters containing 26 structures, highest framenr is 25 -60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (3 ms) -60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset -60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -60: Analyzed 26 frames, last time 0.050 -60: There are 8 clusters containing 26 structures, highest framenr is 25 -60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (3 ms) -60: [----------] 2 tests from ExtractClusterModuleTest (7 ms total) -60: -60: [----------] 2 tests from FreeVolumeModuleTest -60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for 40 particles. These were set to zero. -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: cutoff = 0.18 nm -60: probe_radius = 0 nm -60: seed = 13 -60: ninsert = 1000 probes per nm^3 -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -60: Spoel, Luciano T. Costa -60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -60: Environ. Sci. Technol. (2013) -60: DOI: 10.1021/es4020986 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Free volume 38.02 +/- 0.00 % -60: Total volume 68.92 +/- 0.00 nm^3 -60: Number of molecules 340 total mass 63491.38 Dalton -60: Average molar mass: 186.74 Dalton -60: Density rho: 1529.71 +/- 0.00 nm^3 -60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 -60: Fractional free volume 0.194 +/- 0.000 -60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (48 ms) -60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: cutoff = 0.18 nm -60: probe_radius = 0 nm -60: seed = 17 -60: ninsert = 1000 probes per nm^3 -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -60: Spoel, Luciano T. Costa -60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -60: Environ. Sci. Technol. (2013) -60: DOI: 10.1021/es4020986 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Free volume 38.48 +/- 0.00 % -60: Total volume 68.92 +/- 0.00 nm^3 -60: Number of molecules 340 total mass 63491.38 Dalton -60: Average molar mass: 186.74 Dalton -60: Density rho: 1529.71 +/- 0.00 nm^3 -60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 -60: Fractional free volume 0.200 +/- 0.000 -60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (50 ms) -60: [----------] 2 tests from FreeVolumeModuleTest (98 ms total) -60: -60: [----------] 13 tests from MsdModuleTest -60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (5 ms) -60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (7 ms) -60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) -60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) -60: [ RUN ] MsdModuleTest.multipleGroupsWork -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -561197 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.multipleGroupsWork (60 ms) -60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 -60: Analyzed 21 frames, last time 2.000 -60: Setting the LD random seed to -69239969 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (42 ms) -60: [ RUN ] MsdModuleTest.trestartLessThanDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1074028545 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartLessThanDt (12 ms) -60: [ RUN ] MsdModuleTest.trestartGreaterThanDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to 1986920319 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartGreaterThanDt (44 ms) -60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1670031681 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (91 ms) -60: [ RUN ] MsdModuleTest.molTest -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -1712337003 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.molTest (16 ms) -60: [ RUN ] MsdModuleTest.beginFit -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -134517537 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.beginFit (21 ms) -60: [ RUN ] MsdModuleTest.endFit -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -830808099 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.endFit (34 ms) -60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: NOTE: You provided an index file -60: /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx -60: (with -n), but it was not used by any selection. -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -540833 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (26 ms) -60: [----------] 13 tests from MsdModuleTest (365 ms total) -60: -60: [----------] 9 tests from PairDistanceModuleTest -60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (3 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (2 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (2 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (2 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) -60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (3 ms) -60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) -60: [----------] 9 tests from PairDistanceModuleTest (20 ms total) -60: -60: [----------] 5 tests from RdfModuleTest -60: [ RUN ] RdfModuleTest.BasicTest -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.BasicTest (12 ms) -60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork -60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (10 ms) -60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (11 ms) -60: [ RUN ] RdfModuleTest.CalculatesSurf -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) -60: [ RUN ] RdfModuleTest.CalculatesXY -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.CalculatesXY (14 ms) -60: [----------] 5 tests from RdfModuleTest (54 ms total) -60: -60: [----------] 5 tests from SasaModuleTest -60: [ RUN ] SasaModuleTest.BasicTest -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.BasicTest (7 ms) -60: [ RUN ] SasaModuleTest.HandlesSelectedResidues -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesSelectedResidues (5 ms) -60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (4 ms) -60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (5 ms) -60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (4 ms) -60: [----------] 5 tests from SasaModuleTest (27 ms total) -60: -60: [----------] 8 tests from SelectModuleTest -60: [ RUN ] SelectModuleTest.BasicTest -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.BasicTest (5 ms) -60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) -60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (2 ms) -60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) -60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (2 ms) -60: [ RUN ] SelectModuleTest.NormalizesSizes -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) -60: [ RUN ] SelectModuleTest.WritesResidueNumbers -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) -60: [ RUN ] SelectModuleTest.WritesResidueIndices -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) -60: [----------] 8 tests from SelectModuleTest (21 ms total) -60: -60: [----------] 10 tests from SurfaceAreaTest -60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint -60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) -60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints -60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) -60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius -60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints12 -60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints32 -60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints42 -60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints122 -60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) -60: [ RUN ] SurfaceAreaTest.Computes100Points -60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) -60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC -60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) -60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC -60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) -60: [----------] 10 tests from SurfaceAreaTest (7 ms total) -60: -60: [----------] 4 tests from TopologyInformation -60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile -60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) -60: [ RUN ] TopologyInformation.WorksWithGroFile -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) -60: [ RUN ] TopologyInformation.WorksWithPdbFile -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) -60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file lysozyme.top, line 1465]: -60: System has non-zero total charge: 2.000000 -60: Total charge should normally be an integer. See -60: https://manual.gromacs.org/current/user-guide/floating-point.html -60: for discussion on how close it should be to an integer. -60: -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 465.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: NVE simulation with an initial temperature of zero: will use a Verlet -60: buffer of 10%. Check your energy drift! -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 4 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -60: Setting the LD random seed to -18876513 -60: -60: Generated 330891 of the 330891 non-bonded parameter combinations -60: -60: Generated 330891 of the 330891 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -60: Analysing residue names: -60: There are: 10 Protein residues -60: Analysing Protein... -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (224 ms) -60: [----------] 4 tests from TopologyInformation (226 ms total) -60: -60: [----------] 4 tests from TrajectoryModuleTest -60: [ RUN ] TrajectoryModuleTest.BasicTest -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.BasicTest (17 ms) -60: [ RUN ] TrajectoryModuleTest.PlotsXOnly -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.PlotsXOnly (2 ms) -60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) -60: [ RUN ] TrajectoryModuleTest.HandlesNoForces -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) -60: [----------] 4 tests from TrajectoryModuleTest (23 ms total) -60: -60: [----------] 5 tests from UnionFinderTest -60: [ RUN ] UnionFinderTest.WorksEmpty -60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) -60: [ RUN ] UnionFinderTest.BasicMerges -60: [ OK ] UnionFinderTest.BasicMerges (0 ms) -60: [ RUN ] UnionFinderTest.LargerMerges -60: [ OK ] UnionFinderTest.LargerMerges (0 ms) -60: [ RUN ] UnionFinderTest.LongRightMerge -60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) -60: [ RUN ] UnionFinderTest.LongLeftMerge -60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) -60: [----------] 5 tests from UnionFinderTest (0 ms total) -60: -60: [----------] 1 test from MappedUnionFinderTest -60: [ RUN ] MappedUnionFinderTest.BasicMerges -60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) -60: [----------] 1 test from MappedUnionFinderTest (0 ms total) -60: -60: [----------] 192 tests from MoleculeTests/DsspModuleTest -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (27 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (22 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (27 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (35 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (49 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (25 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (52 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (74 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (17 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (17 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (76 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (24 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (33 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (59 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (78 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (10 ms) -60: [----------] 192 tests from MoleculeTests/DsspModuleTest (3008 ms total) -60: -60: [----------] 3 tests from GyrateTests/GyrateModuleTest -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) -60: [----------] 3 tests from GyrateTests/GyrateModuleTest (14 ms total) -60: -60: [----------] 96 tests from HBondTests/HbondModuleTest -60: [ RUN ] HBondTests/HbondModuleTest.Works/0 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/0 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/1 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/1 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/2 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/2 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/3 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/3 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/4 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/4 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/5 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/5 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/6 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/6 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/7 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/7 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/8 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/8 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/9 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/9 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/10 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/10 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/11 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/11 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/12 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/12 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/13 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/13 (17 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/14 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/14 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/15 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/15 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/16 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/16 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/17 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/17 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/18 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/18 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/19 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/19 (12 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/20 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/20 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/21 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/21 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/22 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/22 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/23 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/23 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/24 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/24 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/25 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/25 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/26 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/26 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/27 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/27 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/28 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/28 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/29 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/29 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/30 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/30 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/31 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/31 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/32 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/32 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/33 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/33 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/34 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/34 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/35 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/35 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/36 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/36 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/37 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/37 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/38 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/38 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/39 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/39 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/40 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/40 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/41 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/41 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/42 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/42 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/43 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/43 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/44 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/44 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/45 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/45 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/46 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/46 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/47 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/47 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/48 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/48 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/49 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/49 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/50 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/50 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/51 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/51 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/52 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/52 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/53 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/53 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/54 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/54 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/55 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/55 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/56 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/56 (44 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/57 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/57 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/58 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/58 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/59 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/59 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/60 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/60 (272 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/61 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/61 (45 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/62 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/62 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/63 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/63 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/64 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/64 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/65 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/65 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/66 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/66 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/67 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/67 (79 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/68 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/68 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/69 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/69 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/70 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/70 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/71 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/71 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/72 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/72 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/73 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/73 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/74 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/74 (42 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/75 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/75 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/76 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/76 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/77 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/77 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/78 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/78 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/79 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/79 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/80 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/80 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/81 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/81 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/82 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/82 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/83 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/83 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/84 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/84 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/85 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/85 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/86 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/86 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/87 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/87 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/88 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/88 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/89 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/89 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/90 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/90 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/91 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/91 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/92 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/92 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/93 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/93 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/94 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/94 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/95 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/95 (39 ms) -60: [----------] 96 tests from HBondTests/HbondModuleTest (3331 ms total) -60: -60: [----------] 4 tests from MoleculeTests/ScatteringModule -60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (7 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: D. T. Cromer, J. B. Mann -60: X-ray scattering factors computed from numerical Hartree-Fock wave functions -60: Acta Cryst. A (1968) -60: DOI: 10.1107/S0567739468000550 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (194 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (6 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: D. T. Cromer, J. B. Mann -60: X-ray scattering factors computed from numerical Hartree-Fock wave functions -60: Acta Cryst. A (1968) -60: DOI: 10.1107/S0567739468000550 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (47 ms) -60: [----------] 4 tests from MoleculeTests/ScatteringModule (256 ms total) -60: -60: [----------] Global test environment tear-down -60: [==========] 393 tests from 21 test suites ran. (7601 ms total) -60: [ PASSED ] 393 tests. -60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 7.62 sec -test 61 - Start 61: EnergyAnalysisUnitTests - -61: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" -61: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/energyanalysis/tests -61: Test timeout computed to be: 30 -61: [==========] Running 12 tests from 5 test suites. -61: [----------] Global test environment set-up. -61: [----------] 2 tests from EnergyTermTest -61: [ RUN ] EnergyTermTest.ConstructWorks -61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) -61: [ RUN ] EnergyTermTest.AddFrameWorks -61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) -61: [----------] 2 tests from EnergyTermTest (0 ms total) -61: -61: [----------] 1 test from DhdlTest -61: [ RUN ] DhdlTest.ExtractDhdl -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file -61: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) -61: Note: file tpx version 110, software tpx version 137 -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 -61: -61: -61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg -61: [ OK ] DhdlTest.ExtractDhdl (6 ms) -61: [----------] 1 test from DhdlTest (6 ms total) -61: -61: [----------] 1 test from OriresTest -61: [ RUN ] OriresTest.ExtractOrires -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file -61: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) -61: Note: file tpx version 111, software tpx version 137 -61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) -61: End your selection with 0 -61: Selecting all 7 orientation restraints -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 -61: [ OK ] OriresTest.ExtractOrires (8 ms) -61: [----------] 1 test from OriresTest (8 ms total) -61: -61: [----------] 5 tests from EnergyTest -61: [ RUN ] EnergyTest.ExtractEnergy -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) -61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -61: [ OK ] EnergyTest.ExtractEnergy (4 ms) -61: [ RUN ] EnergyTest.ExtractEnergyByNumber -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) -61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -61: Pres. DC -268.49 3 8.52175 13.2804 (bar) -61: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) -61: [ RUN ] EnergyTest.ExtractEnergyMixed -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: [ OK ] EnergyTest.ExtractEnergyMixed (5 ms) -61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -61: 37 1/Viscosity 38 T-System 39 Lamb-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -61: -61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets -61: All statistics are over 3 points (frames) -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (2 ms) -61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -61: 37 1/Viscosity 38 T-System 39 Lamb-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -61: -61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets -61: All statistics are over 3 points (frames) -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) -61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) -61: [----------] 5 tests from EnergyTest (22 ms total) -61: -61: [----------] 3 tests from ViscosityTest -61: [ RUN ] ViscosityTest.EinsteinViscosity -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosity (587 ms) -61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (88 ms) -61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (191 ms) -61: [----------] 3 tests from ViscosityTest (867 ms total) -61: -61: [----------] Global test environment tear-down -61: [==========] 12 tests from 5 test suites ran. (904 ms total) -61: [ PASSED ] 12 tests. -61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.92 sec -test 62 - Start 62: ToolUnitTests - -62: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/ToolUnitTests.xml" -62: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests -62: Test timeout computed to be: 1920 -62: [==========] Running 63 tests from 8 test suites. -62: [----------] Global test environment set-up. -62: [----------] 2 tests from DumpTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Setting the LD random seed to -1085804553 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ RUN ] DumpTest.WorksWithTpr -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: -62: inputrec: -62: integrator = md -62: tinit = 0 -62: dt = 0.001 -62: nsteps = 0 -62: init-step = 0 -62: simulation-part = 1 -62: mts = false -62: mass-repartition-factor = 1 -62: comm-mode = Linear -62: nstcomm = 100 -62: bd-fric = 0 -62: ld-seed = -1085804553 -62: emtol = 10 -62: emstep = 0.01 -62: niter = 20 -62: fcstep = 0 -62: nstcgsteep = 1000 -62: nbfgscorr = 10 -62: rtpi = 0.05 -62: nstxout = 0 -62: nstvout = 0 -62: nstfout = 0 -62: nstlog = 1000 -62: nstcalcenergy = 100 -62: nstenergy = 1000 -62: nstxout-compressed = 0 -62: compressed-x-precision = 1000 -62: cutoff-scheme = Verlet -62: nstlist = 10 -62: pbc = xyz -62: periodic-molecules = false -62: verlet-buffer-tolerance = -1 -62: verlet-buffer-pressure-tolerance = 0.5 -62: rlist = 1.1 -62: coulombtype = Cut-off -62: coulomb-modifier = Potential-shift -62: rcoulomb-switch = 0 -62: rcoulomb = 1 -62: epsilon-r = 1 -62: epsilon-rf = inf -62: vdw-type = Cut-off -62: vdw-modifier = Potential-shift -62: rvdw-switch = 0 -62: rvdw = 1 -62: DispCorr = No -62: table-extension = 1 -62: fourierspacing = 0.12 -62: fourier-nx = 0 -62: fourier-ny = 0 -62: fourier-nz = 0 -62: pme-order = 4 -62: ewald-rtol = 1e-05 -62: ewald-rtol-lj = 0.001 -62: lj-pme-comb-rule = Geometric -62: ewald-geometry = 3d -62: epsilon-surface = 0 -62: ensemble-temperature-setting = not available -62: tcoupl = No -62: nsttcouple = -1 -62: nh-chain-length = 0 -62: print-nose-hoover-chain-variables = false -62: pcoupl = No -62: refcoord-scaling = No -62: posres-com: not available -62: posres-comB: not available -62: QMMM = false -62: qm-opts: -62: ngQM = 0 -62: constraint-algorithm = Lincs -62: continuation = false -62: Shake-SOR = false -62: shake-tol = 0.0001 -62: lincs-order = 4 -62: lincs-iter = 1 -62: lincs-warnangle = 30 -62: nwall = 0 -62: wall-type = 9-3 -62: wall-r-linpot = -1 -62: wall-atomtype[0] = -1 -62: wall-atomtype[1] = -1 -62: wall-density[0] = 0 -62: wall-density[1] = 0 -62: wall-ewald-zfac = 3 -62: pull = false -62: awh = false -62: rotation = false -62: interactiveMD = false -62: disre = No -62: disre-weighting = Conservative -62: disre-mixed = false -62: dr-fc = 1000 -62: dr-tau = 0 -62: nstdisreout = 100 -62: orire-fc = 0 -62: orire-tau = 0 -62: nstorireout = 100 -62: free-energy = no -62: cos-acceleration = 0 -62: deform (3x3): -62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: simulated-tempering = false -62: swapcoords = no -62: userint1 = 0 -62: userint2 = 0 -62: userint3 = 0 -62: userint4 = 0 -62: userreal1 = 0 -62: userreal2 = 0 -62: userreal3 = 0 -62: userreal4 = 0 -62: applied-forces: -62: electric-field: -62: x: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: y: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: z: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: density-guided-simulation: -62: active = false -62: group = protein -62: similarity-measure = inner-product -62: atom-spreading-weight = unity -62: force-constant = 1e+09 -62: gaussian-transform-spreading-width = 0.2 -62: gaussian-transform-spreading-range-in-multiples-of-width = 4 -62: reference-density-filename = reference.mrc -62: nst = 1 -62: normalize-densities = true -62: adaptive-force-scaling = false -62: adaptive-force-scaling-time-constant = 4 -62: shift-vector = -62: transformation-matrix = -62: qmmm-cp2k: -62: active = false -62: qmgroup = System -62: qmmethod = PBE -62: qmfilenames = -62: qmcharge = 0 -62: qmmultiplicity = 1 -62: colvars: -62: active = false -62: configfile = -62: seed = -1 -62: nnpot: -62: active = false -62: modelfile = model.pt -62: input-group = System -62: model-input1 = -62: model-input2 = -62: model-input3 = -62: model-input4 = -62: grpopts: -62: nrdf: 465 -62: ref-t: 0 -62: tau-t: 0 -62: annealing: No -62: annealing-npoints: 0 -62: acc: 0 0 0 -62: nfreeze: N N N -62: energygrp-flags[ 0]: 0 -62: header: -62: bIr = present -62: bBox = present -62: bTop = present -62: bX = present -62: bV = present -62: bF = not present -62: natoms = 156 -62: lambda = 0.000000e+00 -62: buffer size = 46382 -62: topology: -62: name="First 10 residues from 1AKI" -62: #atoms = 156 -62: #molblock = 1 -62: molblock (0): -62: moltype = 0 "Protein_chain_B" -62: #molecules = 1 -62: #posres_xA = 0 -62: #posres_xB = 0 -62: bIntermolecularInteractions = false -62: ffparams: -62: atnr=10 -62: ntypes=212 -62: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 -62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 -62: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 -62: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 -62: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 -62: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 -62: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 -62: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 -62: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 -62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 -62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 -62: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 -62: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 -62: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 -62: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 -62: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 -62: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 -62: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 -62: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 -62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 -62: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 -62: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 -62: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 -62: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 -62: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 -62: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 -62: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 -62: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 -62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 -62: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 -62: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 -62: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 -62: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 -62: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 -62: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 -62: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 -62: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 -62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 -62: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 -62: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 -62: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 -62: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 -62: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 -62: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 -62: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 -62: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 -62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 -62: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 -62: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 -62: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 -62: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 -62: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 -62: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 -62: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 -62: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 -62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 -62: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 -62: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 -62: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 -62: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 -62: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 -62: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 -62: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 -62: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 -62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 -62: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 -62: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 -62: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 -62: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 -62: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 -62: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 -62: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 -62: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 -62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 -62: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 -62: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 -62: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 -62: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 -62: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 -62: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 -62: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 -62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 -62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 -62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 -62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 -62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 -62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 -62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 -62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 -62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 -62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 -62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 -62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 -62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 -62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 -62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 -62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 -62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 -62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 -62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 -62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 -62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 -62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 -62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 -62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 -62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 -62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 -62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 -62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 -62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 -62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 -62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 -62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 -62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 -62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 -62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 -62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 -62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 -62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 -62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 -62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 -62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 -62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 -62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 -62: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 -62: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 -62: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 -62: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 -62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 -62: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 -62: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 -62: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 -62: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 -62: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 -62: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 -62: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 -62: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 -62: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 -62: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 -62: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 -62: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 -62: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 -62: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 -62: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 -62: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 -62: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 -62: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 -62: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 -62: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 -62: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 -62: reppow = 12 -62: fudgeQQ = 0.5 -62: cmap -62: moltype (0): -62: name="Protein_chain_B" -62: atoms: -62: atom (156): -62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} -62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} -62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} -62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} -62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} -62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} -62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} -62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} -62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} -62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} -62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} -62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} -62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} -62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} -62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} -62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} -62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} -62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} -62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} -62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} -62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} -62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} -62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} -62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} -62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} -62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} -62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} -62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} -62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} -62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} -62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} -62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} -62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} -62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} -62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} -62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} -62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} -62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} -62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} -62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} -62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} -62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} -62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} -62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} -62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} -62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} -62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} -62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} -62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} -62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} -62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} -62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} -62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} -62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} -62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} -62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} -62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} -62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} -62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} -62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} -62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} -62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} -62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} -62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} -62: atom (156): -62: atom[0]={name="N"} -62: atom[1]={name="H1"} -62: atom[2]={name="H2"} -62: atom[3]={name="H3"} -62: atom[4]={name="CA"} -62: atom[5]={name="HA"} -62: atom[6]={name="CB"} -62: atom[7]={name="HB1"} -62: atom[8]={name="HB2"} -62: atom[9]={name="CG"} -62: atom[10]={name="HG1"} -62: atom[11]={name="HG2"} -62: atom[12]={name="CD"} -62: atom[13]={name="HD1"} -62: atom[14]={name="HD2"} -62: atom[15]={name="CE"} -62: atom[16]={name="HE1"} -62: atom[17]={name="HE2"} -62: atom[18]={name="NZ"} -62: atom[19]={name="HZ1"} -62: atom[20]={name="HZ2"} -62: atom[21]={name="HZ3"} -62: atom[22]={name="C"} -62: atom[23]={name="O"} -62: atom[24]={name="N"} -62: atom[25]={name="H"} -62: atom[26]={name="CA"} -62: atom[27]={name="HA"} -62: atom[28]={name="CB"} -62: atom[29]={name="HB"} -62: atom[30]={name="CG1"} -62: atom[31]={name="HG11"} -62: atom[32]={name="HG12"} -62: atom[33]={name="HG13"} -62: atom[34]={name="CG2"} -62: atom[35]={name="HG21"} -62: atom[36]={name="HG22"} -62: atom[37]={name="HG23"} -62: atom[38]={name="C"} -62: atom[39]={name="O"} -62: atom[40]={name="N"} -62: atom[41]={name="H"} -62: atom[42]={name="CA"} -62: atom[43]={name="HA"} -62: atom[44]={name="CB"} -62: atom[45]={name="HB1"} -62: atom[46]={name="HB2"} -62: atom[47]={name="CG"} -62: atom[48]={name="CD1"} -62: atom[49]={name="HD1"} -62: atom[50]={name="CD2"} -62: atom[51]={name="HD2"} -62: atom[52]={name="CE1"} -62: atom[53]={name="HE1"} -62: atom[54]={name="CE2"} -62: atom[55]={name="HE2"} -62: atom[56]={name="CZ"} -62: atom[57]={name="HZ"} -62: atom[58]={name="C"} -62: atom[59]={name="O"} -62: atom[60]={name="N"} -62: atom[61]={name="H"} -62: atom[62]={name="CA"} -62: atom[63]={name="HA1"} -62: atom[64]={name="HA2"} -62: atom[65]={name="C"} -62: atom[66]={name="O"} -62: atom[67]={name="N"} -62: atom[68]={name="H"} -62: atom[69]={name="CA"} -62: atom[70]={name="HA"} -62: atom[71]={name="CB"} -62: atom[72]={name="HB1"} -62: atom[73]={name="HB2"} -62: atom[74]={name="CG"} -62: atom[75]={name="HG1"} -62: atom[76]={name="HG2"} -62: atom[77]={name="CD"} -62: atom[78]={name="HD1"} -62: atom[79]={name="HD2"} -62: atom[80]={name="NE"} -62: atom[81]={name="HE"} -62: atom[82]={name="CZ"} -62: atom[83]={name="NH1"} -62: atom[84]={name="HH11"} -62: atom[85]={name="HH12"} -62: atom[86]={name="NH2"} -62: atom[87]={name="HH21"} -62: atom[88]={name="HH22"} -62: atom[89]={name="C"} -62: atom[90]={name="O"} -62: atom[91]={name="N"} -62: atom[92]={name="H"} -62: atom[93]={name="CA"} -62: atom[94]={name="HA"} -62: atom[95]={name="CB"} -62: atom[96]={name="HB1"} -62: atom[97]={name="HB2"} -62: atom[98]={name="SG"} -62: atom[99]={name="HG"} -62: atom[100]={name="C"} -62: atom[101]={name="O"} -62: atom[102]={name="N"} -62: atom[103]={name="H"} -62: atom[104]={name="CA"} -62: atom[105]={name="HA"} -62: atom[106]={name="CB"} -62: atom[107]={name="HB1"} -62: atom[108]={name="HB2"} -62: atom[109]={name="CG"} -62: atom[110]={name="HG1"} -62: atom[111]={name="HG2"} -62: atom[112]={name="CD"} -62: atom[113]={name="OE1"} -62: atom[114]={name="OE2"} -62: atom[115]={name="C"} -62: atom[116]={name="O"} -62: atom[117]={name="N"} -62: atom[118]={name="H"} -62: atom[119]={name="CA"} -62: atom[120]={name="HA"} -62: atom[121]={name="CB"} -62: atom[122]={name="HB1"} -62: atom[123]={name="HB2"} -62: atom[124]={name="CG"} -62: atom[125]={name="HG"} -62: atom[126]={name="CD1"} -62: atom[127]={name="HD11"} -62: atom[128]={name="HD12"} -62: atom[129]={name="HD13"} -62: atom[130]={name="CD2"} -62: atom[131]={name="HD21"} -62: atom[132]={name="HD22"} -62: atom[133]={name="HD23"} -62: atom[134]={name="C"} -62: atom[135]={name="O"} -62: atom[136]={name="N"} -62: atom[137]={name="H"} -62: atom[138]={name="CA"} -62: atom[139]={name="HA"} -62: atom[140]={name="CB"} -62: atom[141]={name="HB1"} -62: atom[142]={name="HB2"} -62: atom[143]={name="HB3"} -62: atom[144]={name="C"} -62: atom[145]={name="O"} -62: atom[146]={name="N"} -62: atom[147]={name="H"} -62: atom[148]={name="CA"} -62: atom[149]={name="HA"} -62: atom[150]={name="CB"} -62: atom[151]={name="HB1"} -62: atom[152]={name="HB2"} -62: atom[153]={name="HB3"} -62: atom[154]={name="C"} -62: atom[155]={name="O"} -62: type (156): -62: type[0]={name="opls_287",nameB="opls_287"} -62: type[1]={name="opls_290",nameB="opls_290"} -62: type[2]={name="opls_290",nameB="opls_290"} -62: type[3]={name="opls_290",nameB="opls_290"} -62: type[4]={name="opls_293B",nameB="opls_293B"} -62: type[5]={name="opls_140",nameB="opls_140"} -62: type[6]={name="opls_136",nameB="opls_136"} -62: type[7]={name="opls_140",nameB="opls_140"} -62: type[8]={name="opls_140",nameB="opls_140"} -62: type[9]={name="opls_136",nameB="opls_136"} -62: type[10]={name="opls_140",nameB="opls_140"} -62: type[11]={name="opls_140",nameB="opls_140"} -62: type[12]={name="opls_136",nameB="opls_136"} -62: type[13]={name="opls_140",nameB="opls_140"} -62: type[14]={name="opls_140",nameB="opls_140"} -62: type[15]={name="opls_292",nameB="opls_292"} -62: type[16]={name="opls_140",nameB="opls_140"} -62: type[17]={name="opls_140",nameB="opls_140"} -62: type[18]={name="opls_287",nameB="opls_287"} -62: type[19]={name="opls_290",nameB="opls_290"} -62: type[20]={name="opls_290",nameB="opls_290"} -62: type[21]={name="opls_290",nameB="opls_290"} -62: type[22]={name="opls_235",nameB="opls_235"} -62: type[23]={name="opls_236",nameB="opls_236"} -62: type[24]={name="opls_238",nameB="opls_238"} -62: type[25]={name="opls_241",nameB="opls_241"} -62: type[26]={name="opls_224B",nameB="opls_224B"} -62: type[27]={name="opls_140",nameB="opls_140"} -62: type[28]={name="opls_137",nameB="opls_137"} -62: type[29]={name="opls_140",nameB="opls_140"} -62: type[30]={name="opls_135",nameB="opls_135"} -62: type[31]={name="opls_140",nameB="opls_140"} -62: type[32]={name="opls_140",nameB="opls_140"} -62: type[33]={name="opls_140",nameB="opls_140"} -62: type[34]={name="opls_135",nameB="opls_135"} -62: type[35]={name="opls_140",nameB="opls_140"} -62: type[36]={name="opls_140",nameB="opls_140"} -62: type[37]={name="opls_140",nameB="opls_140"} -62: type[38]={name="opls_235",nameB="opls_235"} -62: type[39]={name="opls_236",nameB="opls_236"} -62: type[40]={name="opls_238",nameB="opls_238"} -62: type[41]={name="opls_241",nameB="opls_241"} -62: type[42]={name="opls_224B",nameB="opls_224B"} -62: type[43]={name="opls_140",nameB="opls_140"} -62: type[44]={name="opls_149",nameB="opls_149"} -62: type[45]={name="opls_140",nameB="opls_140"} -62: type[46]={name="opls_140",nameB="opls_140"} -62: type[47]={name="opls_145",nameB="opls_145"} -62: type[48]={name="opls_145",nameB="opls_145"} -62: type[49]={name="opls_146",nameB="opls_146"} -62: type[50]={name="opls_145",nameB="opls_145"} -62: type[51]={name="opls_146",nameB="opls_146"} -62: type[52]={name="opls_145",nameB="opls_145"} -62: type[53]={name="opls_146",nameB="opls_146"} -62: type[54]={name="opls_145",nameB="opls_145"} -62: type[55]={name="opls_146",nameB="opls_146"} -62: type[56]={name="opls_145",nameB="opls_145"} -62: type[57]={name="opls_146",nameB="opls_146"} -62: type[58]={name="opls_235",nameB="opls_235"} -62: type[59]={name="opls_236",nameB="opls_236"} -62: type[60]={name="opls_238",nameB="opls_238"} -62: type[61]={name="opls_241",nameB="opls_241"} -62: type[62]={name="opls_223B",nameB="opls_223B"} -62: type[63]={name="opls_140",nameB="opls_140"} -62: type[64]={name="opls_140",nameB="opls_140"} -62: type[65]={name="opls_235",nameB="opls_235"} -62: type[66]={name="opls_236",nameB="opls_236"} -62: type[67]={name="opls_238",nameB="opls_238"} -62: type[68]={name="opls_241",nameB="opls_241"} -62: type[69]={name="opls_224B",nameB="opls_224B"} -62: type[70]={name="opls_140",nameB="opls_140"} -62: type[71]={name="opls_136",nameB="opls_136"} -62: type[72]={name="opls_140",nameB="opls_140"} -62: type[73]={name="opls_140",nameB="opls_140"} -62: type[74]={name="opls_308",nameB="opls_308"} -62: type[75]={name="opls_140",nameB="opls_140"} -62: type[76]={name="opls_140",nameB="opls_140"} -62: type[77]={name="opls_307",nameB="opls_307"} -62: type[78]={name="opls_140",nameB="opls_140"} -62: type[79]={name="opls_140",nameB="opls_140"} -62: type[80]={name="opls_303",nameB="opls_303"} -62: type[81]={name="opls_304",nameB="opls_304"} -62: type[82]={name="opls_302",nameB="opls_302"} -62: type[83]={name="opls_300",nameB="opls_300"} -62: type[84]={name="opls_301",nameB="opls_301"} -62: type[85]={name="opls_301",nameB="opls_301"} -62: type[86]={name="opls_300",nameB="opls_300"} -62: type[87]={name="opls_301",nameB="opls_301"} -62: type[88]={name="opls_301",nameB="opls_301"} -62: type[89]={name="opls_235",nameB="opls_235"} -62: type[90]={name="opls_236",nameB="opls_236"} -62: type[91]={name="opls_238",nameB="opls_238"} -62: type[92]={name="opls_241",nameB="opls_241"} -62: type[93]={name="opls_224B",nameB="opls_224B"} -62: type[94]={name="opls_140",nameB="opls_140"} -62: type[95]={name="opls_206",nameB="opls_206"} -62: type[96]={name="opls_140",nameB="opls_140"} -62: type[97]={name="opls_140",nameB="opls_140"} -62: type[98]={name="opls_200",nameB="opls_200"} -62: type[99]={name="opls_204",nameB="opls_204"} -62: type[100]={name="opls_235",nameB="opls_235"} -62: type[101]={name="opls_236",nameB="opls_236"} -62: type[102]={name="opls_238",nameB="opls_238"} -62: type[103]={name="opls_241",nameB="opls_241"} -62: type[104]={name="opls_224B",nameB="opls_224B"} -62: type[105]={name="opls_140",nameB="opls_140"} -62: type[106]={name="opls_136",nameB="opls_136"} -62: type[107]={name="opls_140",nameB="opls_140"} -62: type[108]={name="opls_140",nameB="opls_140"} -62: type[109]={name="opls_274",nameB="opls_274"} -62: type[110]={name="opls_140",nameB="opls_140"} -62: type[111]={name="opls_140",nameB="opls_140"} -62: type[112]={name="opls_271",nameB="opls_271"} -62: type[113]={name="opls_272",nameB="opls_272"} -62: type[114]={name="opls_272",nameB="opls_272"} -62: type[115]={name="opls_235",nameB="opls_235"} -62: type[116]={name="opls_236",nameB="opls_236"} -62: type[117]={name="opls_238",nameB="opls_238"} -62: type[118]={name="opls_241",nameB="opls_241"} -62: type[119]={name="opls_224B",nameB="opls_224B"} -62: type[120]={name="opls_140",nameB="opls_140"} -62: type[121]={name="opls_136",nameB="opls_136"} -62: type[122]={name="opls_140",nameB="opls_140"} -62: type[123]={name="opls_140",nameB="opls_140"} -62: type[124]={name="opls_137",nameB="opls_137"} -62: type[125]={name="opls_140",nameB="opls_140"} -62: type[126]={name="opls_135",nameB="opls_135"} -62: type[127]={name="opls_140",nameB="opls_140"} -62: type[128]={name="opls_140",nameB="opls_140"} -62: type[129]={name="opls_140",nameB="opls_140"} -62: type[130]={name="opls_135",nameB="opls_135"} -62: type[131]={name="opls_140",nameB="opls_140"} -62: type[132]={name="opls_140",nameB="opls_140"} -62: type[133]={name="opls_140",nameB="opls_140"} -62: type[134]={name="opls_235",nameB="opls_235"} -62: type[135]={name="opls_236",nameB="opls_236"} -62: type[136]={name="opls_238",nameB="opls_238"} -62: type[137]={name="opls_241",nameB="opls_241"} -62: type[138]={name="opls_224B",nameB="opls_224B"} -62: type[139]={name="opls_140",nameB="opls_140"} -62: type[140]={name="opls_135",nameB="opls_135"} -62: type[141]={name="opls_140",nameB="opls_140"} -62: type[142]={name="opls_140",nameB="opls_140"} -62: type[143]={name="opls_140",nameB="opls_140"} -62: type[144]={name="opls_235",nameB="opls_235"} -62: type[145]={name="opls_236",nameB="opls_236"} -62: type[146]={name="opls_238",nameB="opls_238"} -62: type[147]={name="opls_241",nameB="opls_241"} -62: type[148]={name="opls_224B",nameB="opls_224B"} -62: type[149]={name="opls_140",nameB="opls_140"} -62: type[150]={name="opls_135",nameB="opls_135"} -62: type[151]={name="opls_140",nameB="opls_140"} -62: type[152]={name="opls_140",nameB="opls_140"} -62: type[153]={name="opls_140",nameB="opls_140"} -62: type[154]={name="opls_235",nameB="opls_235"} -62: type[155]={name="opls_236",nameB="opls_236"} -62: residue (10): -62: residue[0]={name="LYS", nr=1, ic=' '} -62: residue[1]={name="VAL", nr=2, ic=' '} -62: residue[2]={name="PHE", nr=3, ic=' '} -62: residue[3]={name="GLY", nr=4, ic=' '} -62: residue[4]={name="ARG", nr=5, ic=' '} -62: residue[5]={name="CYS", nr=6, ic=' '} -62: residue[6]={name="GLU", nr=7, ic=' '} -62: residue[7]={name="LEU", nr=8, ic=' '} -62: residue[8]={name="ALA", nr=9, ic=' '} -62: residue[9]={name="ALA", nr=10, ic=' '} -62: excls: -62: numLists=156 -62: numElements=1828 -62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, -62: 23, 24, 25, 26} -62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, -62: 14, 15, 22, 23, 24} -62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -62: 16, 17, 18, 22} -62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, -62: 17, 18, 19, 20, 21} -62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, -62: 20, 21} -62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, -62: 26, 27, 28, 38} -62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} -62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, -62: 30, 34, 38, 39, 40} -62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} -62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, -62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} -62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -62: 40} -62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, -62: 34, 35, 36, 37, 38, 39, 40} -62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -62: 40, 41, 42, 43, 44, 58} -62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} -62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, -62: 45, 46, 47, 58, 59, 60} -62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} -62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, -62: 48, 50, 58, 59, 60, 61, 62} -62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -62: 60} -62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, -62: 50, 51, 52, 54, 58, 59, 60} -62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, -62: 52, 53, 54, 55, 56, 58} -62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, -62: 54, 56, 57} -62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} -62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, -62: 55, 56, 57} -62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} -62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} -62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} -62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} -62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} -62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} -62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} -62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -62: 60, 61, 62, 63, 64, 65} -62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} -62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, -62: 65, 66, 67} -62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} -62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, -62: 68, 69} -62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, -62: 70, 71, 89} -62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} -62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, -62: 72, 73, 74, 89, 90, 91} -62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} -62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, -62: 75, 76, 77, 89, 90, 91, 92, 93} -62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -62: 91} -62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, -62: 77, 78, 79, 80, 89, 90, 91} -62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, -62: 79, 80, 81, 82, 89} -62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, -62: 81, 82, 83, 86} -62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, -62: 84, 85, 86, 87, 88} -62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} -62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, -62: 87, 88} -62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -62: excls[84][num=6]={80, 82, 83, 84, 85, 86} -62: excls[85][num=6]={80, 82, 83, 84, 85, 86} -62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -62: excls[87][num=6]={80, 82, 83, 86, 87, 88} -62: excls[88][num=6]={80, 82, 83, 86, 87, 88} -62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -62: 91, 92, 93, 94, 95, 100} -62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} -62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, -62: 96, 97, 98, 100, 101, 102} -62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} -62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, -62: 99, 100, 101, 102, 103, 104} -62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -62: 102} -62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, -62: 101, 102} -62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[99][num=6]={93, 95, 96, 97, 98, 99} -62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -62: 102, 103, 104, 105, 106, 115} -62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} -62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, -62: 106, 107, 108, 109, 115, 116, 117} -62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} -62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, -62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} -62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 115, 116, 117} -62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 110, 111, 112, 113, 114, 115, 116, 117} -62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 115} -62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 115} -62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 113, 114, 115} -62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} -62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} -62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 115, 116, 117, 118, 119, 120, 121, 134} -62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} -62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, -62: 120, 121, 122, 123, 124, 134, 135, 136} -62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} -62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, -62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} -62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 134, 135, 136} -62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} -62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 130, 134} -62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 130, 134} -62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 127, 128, 129, 130, 131, 132, 133, 134} -62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 134, 135, 136, 137, 138, 139, 140, 144} -62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} -62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, -62: 139, 140, 141, 142, 143, 144, 145, 146} -62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} -62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, -62: 142, 143, 144, 145, 146, 147, 148} -62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146} -62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146} -62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146, 147, 148, 149, 150, 154} -62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} -62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, -62: 149, 150, 151, 152, 153, 154, 155} -62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} -62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, -62: 152, 153, 154, 155} -62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[155][num=6]={146, 148, 149, 150, 154, 155} -62: Bond: -62: nr: 468 -62: iatoms: -62: 0 type=100 (BONDS) 0 1 -62: 1 type=100 (BONDS) 0 2 -62: 2 type=100 (BONDS) 0 3 -62: 3 type=101 (BONDS) 0 4 -62: 4 type=102 (BONDS) 4 5 -62: 5 type=103 (BONDS) 4 6 -62: 6 type=104 (BONDS) 4 22 -62: 7 type=102 (BONDS) 6 7 -62: 8 type=102 (BONDS) 6 8 -62: 9 type=103 (BONDS) 6 9 -62: 10 type=102 (BONDS) 9 10 -62: 11 type=102 (BONDS) 9 11 -62: 12 type=103 (BONDS) 9 12 -62: 13 type=102 (BONDS) 12 13 -62: 14 type=102 (BONDS) 12 14 -62: 15 type=103 (BONDS) 12 15 -62: 16 type=102 (BONDS) 15 16 -62: 17 type=102 (BONDS) 15 17 -62: 18 type=101 (BONDS) 15 18 -62: 19 type=100 (BONDS) 18 19 -62: 20 type=100 (BONDS) 18 20 -62: 21 type=100 (BONDS) 18 21 -62: 22 type=105 (BONDS) 22 23 -62: 23 type=106 (BONDS) 22 24 -62: 24 type=100 (BONDS) 24 25 -62: 25 type=107 (BONDS) 24 26 -62: 26 type=102 (BONDS) 26 27 -62: 27 type=103 (BONDS) 26 28 -62: 28 type=104 (BONDS) 26 38 -62: 29 type=102 (BONDS) 28 29 -62: 30 type=103 (BONDS) 28 30 -62: 31 type=103 (BONDS) 28 34 -62: 32 type=102 (BONDS) 30 31 -62: 33 type=102 (BONDS) 30 32 -62: 34 type=102 (BONDS) 30 33 -62: 35 type=102 (BONDS) 34 35 -62: 36 type=102 (BONDS) 34 36 -62: 37 type=102 (BONDS) 34 37 -62: 38 type=105 (BONDS) 38 39 -62: 39 type=106 (BONDS) 38 40 -62: 40 type=100 (BONDS) 40 41 -62: 41 type=107 (BONDS) 40 42 -62: 42 type=102 (BONDS) 42 43 -62: 43 type=103 (BONDS) 42 44 -62: 44 type=104 (BONDS) 42 58 -62: 45 type=102 (BONDS) 44 45 -62: 46 type=102 (BONDS) 44 46 -62: 47 type=108 (BONDS) 44 47 -62: 48 type=109 (BONDS) 47 48 -62: 49 type=109 (BONDS) 47 50 -62: 50 type=110 (BONDS) 48 49 -62: 51 type=109 (BONDS) 48 52 -62: 52 type=110 (BONDS) 50 51 -62: 53 type=109 (BONDS) 50 54 -62: 54 type=110 (BONDS) 52 53 -62: 55 type=109 (BONDS) 52 56 -62: 56 type=110 (BONDS) 54 55 -62: 57 type=109 (BONDS) 54 56 -62: 58 type=110 (BONDS) 56 57 -62: 59 type=105 (BONDS) 58 59 -62: 60 type=106 (BONDS) 58 60 -62: 61 type=100 (BONDS) 60 61 -62: 62 type=107 (BONDS) 60 62 -62: 63 type=102 (BONDS) 62 63 -62: 64 type=102 (BONDS) 62 64 -62: 65 type=104 (BONDS) 62 65 -62: 66 type=105 (BONDS) 65 66 -62: 67 type=106 (BONDS) 65 67 -62: 68 type=100 (BONDS) 67 68 -62: 69 type=107 (BONDS) 67 69 -62: 70 type=102 (BONDS) 69 70 -62: 71 type=103 (BONDS) 69 71 -62: 72 type=104 (BONDS) 69 89 -62: 73 type=102 (BONDS) 71 72 -62: 74 type=102 (BONDS) 71 73 -62: 75 type=103 (BONDS) 71 74 -62: 76 type=102 (BONDS) 74 75 -62: 77 type=102 (BONDS) 74 76 -62: 78 type=103 (BONDS) 74 77 -62: 79 type=102 (BONDS) 77 78 -62: 80 type=102 (BONDS) 77 79 -62: 81 type=111 (BONDS) 77 80 -62: 82 type=100 (BONDS) 80 81 -62: 83 type=112 (BONDS) 80 82 -62: 84 type=112 (BONDS) 82 83 -62: 85 type=112 (BONDS) 82 86 -62: 86 type=100 (BONDS) 83 84 -62: 87 type=100 (BONDS) 83 85 -62: 88 type=100 (BONDS) 86 87 -62: 89 type=100 (BONDS) 86 88 -62: 90 type=105 (BONDS) 89 90 -62: 91 type=106 (BONDS) 89 91 -62: 92 type=100 (BONDS) 91 92 -62: 93 type=107 (BONDS) 91 93 -62: 94 type=102 (BONDS) 93 94 -62: 95 type=103 (BONDS) 93 95 -62: 96 type=104 (BONDS) 93 100 -62: 97 type=102 (BONDS) 95 96 -62: 98 type=102 (BONDS) 95 97 -62: 99 type=113 (BONDS) 95 98 -62: 100 type=114 (BONDS) 98 99 -62: 101 type=105 (BONDS) 100 101 -62: 102 type=106 (BONDS) 100 102 -62: 103 type=100 (BONDS) 102 103 -62: 104 type=107 (BONDS) 102 104 -62: 105 type=102 (BONDS) 104 105 -62: 106 type=103 (BONDS) 104 106 -62: 107 type=104 (BONDS) 104 115 -62: 108 type=102 (BONDS) 106 107 -62: 109 type=102 (BONDS) 106 108 -62: 110 type=103 (BONDS) 106 109 -62: 111 type=102 (BONDS) 109 110 -62: 112 type=102 (BONDS) 109 111 -62: 113 type=104 (BONDS) 109 112 -62: 114 type=115 (BONDS) 112 113 -62: 115 type=115 (BONDS) 112 114 -62: 116 type=105 (BONDS) 115 116 -62: 117 type=106 (BONDS) 115 117 -62: 118 type=100 (BONDS) 117 118 -62: 119 type=107 (BONDS) 117 119 -62: 120 type=102 (BONDS) 119 120 -62: 121 type=103 (BONDS) 119 121 -62: 122 type=104 (BONDS) 119 134 -62: 123 type=102 (BONDS) 121 122 -62: 124 type=102 (BONDS) 121 123 -62: 125 type=103 (BONDS) 121 124 -62: 126 type=102 (BONDS) 124 125 -62: 127 type=103 (BONDS) 124 126 -62: 128 type=103 (BONDS) 124 130 -62: 129 type=102 (BONDS) 126 127 -62: 130 type=102 (BONDS) 126 128 -62: 131 type=102 (BONDS) 126 129 -62: 132 type=102 (BONDS) 130 131 -62: 133 type=102 (BONDS) 130 132 -62: 134 type=102 (BONDS) 130 133 -62: 135 type=105 (BONDS) 134 135 -62: 136 type=106 (BONDS) 134 136 -62: 137 type=100 (BONDS) 136 137 -62: 138 type=107 (BONDS) 136 138 -62: 139 type=102 (BONDS) 138 139 -62: 140 type=103 (BONDS) 138 140 -62: 141 type=104 (BONDS) 138 144 -62: 142 type=102 (BONDS) 140 141 -62: 143 type=102 (BONDS) 140 142 -62: 144 type=102 (BONDS) 140 143 -62: 145 type=105 (BONDS) 144 145 -62: 146 type=106 (BONDS) 144 146 -62: 147 type=100 (BONDS) 146 147 -62: 148 type=107 (BONDS) 146 148 -62: 149 type=102 (BONDS) 148 149 -62: 150 type=103 (BONDS) 148 150 -62: 151 type=104 (BONDS) 148 154 -62: 152 type=102 (BONDS) 150 151 -62: 153 type=102 (BONDS) 150 152 -62: 154 type=102 (BONDS) 150 153 -62: 155 type=105 (BONDS) 154 155 -62: G96Bond: -62: nr: 0 -62: Morse: -62: nr: 0 -62: Cubic Bonds: -62: nr: 0 -62: Connect Bonds: -62: nr: 0 -62: Harmonic Pot.: -62: nr: 0 -62: FENE Bonds: -62: nr: 0 -62: Tab. Bonds: -62: nr: 0 -62: Tab. Bonds NC: -62: nr: 0 -62: Restraint Pot.: -62: nr: 0 -62: Angle: -62: nr: 1124 -62: iatoms: -62: 0 type=116 (ANGLES) 1 0 2 -62: 1 type=116 (ANGLES) 1 0 3 -62: 2 type=116 (ANGLES) 1 0 4 -62: 3 type=116 (ANGLES) 2 0 3 -62: 4 type=116 (ANGLES) 2 0 4 -62: 5 type=116 (ANGLES) 3 0 4 -62: 6 type=116 (ANGLES) 0 4 5 -62: 7 type=117 (ANGLES) 0 4 6 -62: 8 type=117 (ANGLES) 0 4 22 -62: 9 type=118 (ANGLES) 5 4 6 -62: 10 type=116 (ANGLES) 5 4 22 -62: 11 type=119 (ANGLES) 6 4 22 -62: 12 type=118 (ANGLES) 4 6 7 -62: 13 type=118 (ANGLES) 4 6 8 -62: 14 type=120 (ANGLES) 4 6 9 -62: 15 type=121 (ANGLES) 7 6 8 -62: 16 type=118 (ANGLES) 7 6 9 -62: 17 type=118 (ANGLES) 8 6 9 -62: 18 type=118 (ANGLES) 6 9 10 -62: 19 type=118 (ANGLES) 6 9 11 -62: 20 type=120 (ANGLES) 6 9 12 -62: 21 type=121 (ANGLES) 10 9 11 -62: 22 type=118 (ANGLES) 10 9 12 -62: 23 type=118 (ANGLES) 11 9 12 -62: 24 type=118 (ANGLES) 9 12 13 -62: 25 type=118 (ANGLES) 9 12 14 -62: 26 type=120 (ANGLES) 9 12 15 -62: 27 type=121 (ANGLES) 13 12 14 -62: 28 type=118 (ANGLES) 13 12 15 -62: 29 type=118 (ANGLES) 14 12 15 -62: 30 type=118 (ANGLES) 12 15 16 -62: 31 type=118 (ANGLES) 12 15 17 -62: 32 type=117 (ANGLES) 12 15 18 -62: 33 type=121 (ANGLES) 16 15 17 -62: 34 type=116 (ANGLES) 16 15 18 -62: 35 type=116 (ANGLES) 17 15 18 -62: 36 type=116 (ANGLES) 15 18 19 -62: 37 type=116 (ANGLES) 15 18 20 -62: 38 type=116 (ANGLES) 15 18 21 -62: 39 type=116 (ANGLES) 19 18 20 -62: 40 type=116 (ANGLES) 19 18 21 -62: 41 type=116 (ANGLES) 20 18 21 -62: 42 type=122 (ANGLES) 4 22 23 -62: 43 type=123 (ANGLES) 4 22 24 -62: 44 type=124 (ANGLES) 23 22 24 -62: 45 type=125 (ANGLES) 22 24 25 -62: 46 type=126 (ANGLES) 22 24 26 -62: 47 type=127 (ANGLES) 25 24 26 -62: 48 type=116 (ANGLES) 24 26 27 -62: 49 type=128 (ANGLES) 24 26 28 -62: 50 type=129 (ANGLES) 24 26 38 -62: 51 type=118 (ANGLES) 27 26 28 -62: 52 type=116 (ANGLES) 27 26 38 -62: 53 type=119 (ANGLES) 28 26 38 -62: 54 type=118 (ANGLES) 26 28 29 -62: 55 type=120 (ANGLES) 26 28 30 -62: 56 type=120 (ANGLES) 26 28 34 -62: 57 type=118 (ANGLES) 29 28 30 -62: 58 type=118 (ANGLES) 29 28 34 -62: 59 type=120 (ANGLES) 30 28 34 -62: 60 type=118 (ANGLES) 28 30 31 -62: 61 type=118 (ANGLES) 28 30 32 -62: 62 type=118 (ANGLES) 28 30 33 -62: 63 type=121 (ANGLES) 31 30 32 -62: 64 type=121 (ANGLES) 31 30 33 -62: 65 type=121 (ANGLES) 32 30 33 -62: 66 type=118 (ANGLES) 28 34 35 -62: 67 type=118 (ANGLES) 28 34 36 -62: 68 type=118 (ANGLES) 28 34 37 -62: 69 type=121 (ANGLES) 35 34 36 -62: 70 type=121 (ANGLES) 35 34 37 -62: 71 type=121 (ANGLES) 36 34 37 -62: 72 type=122 (ANGLES) 26 38 39 -62: 73 type=123 (ANGLES) 26 38 40 -62: 74 type=124 (ANGLES) 39 38 40 -62: 75 type=125 (ANGLES) 38 40 41 -62: 76 type=126 (ANGLES) 38 40 42 -62: 77 type=127 (ANGLES) 41 40 42 -62: 78 type=116 (ANGLES) 40 42 43 -62: 79 type=128 (ANGLES) 40 42 44 -62: 80 type=129 (ANGLES) 40 42 58 -62: 81 type=118 (ANGLES) 43 42 44 -62: 82 type=116 (ANGLES) 43 42 58 -62: 83 type=119 (ANGLES) 44 42 58 -62: 84 type=118 (ANGLES) 42 44 45 -62: 85 type=118 (ANGLES) 42 44 46 -62: 86 type=130 (ANGLES) 42 44 47 -62: 87 type=121 (ANGLES) 45 44 46 -62: 88 type=116 (ANGLES) 45 44 47 -62: 89 type=116 (ANGLES) 46 44 47 -62: 90 type=131 (ANGLES) 44 47 48 -62: 91 type=131 (ANGLES) 44 47 50 -62: 92 type=132 (ANGLES) 48 47 50 -62: 93 type=133 (ANGLES) 47 48 49 -62: 94 type=132 (ANGLES) 47 48 52 -62: 95 type=133 (ANGLES) 49 48 52 -62: 96 type=133 (ANGLES) 47 50 51 -62: 97 type=132 (ANGLES) 47 50 54 -62: 98 type=133 (ANGLES) 51 50 54 -62: 99 type=133 (ANGLES) 48 52 53 -62: 100 type=132 (ANGLES) 48 52 56 -62: 101 type=133 (ANGLES) 53 52 56 -62: 102 type=133 (ANGLES) 50 54 55 -62: 103 type=132 (ANGLES) 50 54 56 -62: 104 type=133 (ANGLES) 55 54 56 -62: 105 type=132 (ANGLES) 52 56 54 -62: 106 type=133 (ANGLES) 52 56 57 -62: 107 type=133 (ANGLES) 54 56 57 -62: 108 type=122 (ANGLES) 42 58 59 -62: 109 type=123 (ANGLES) 42 58 60 -62: 110 type=124 (ANGLES) 59 58 60 -62: 111 type=125 (ANGLES) 58 60 61 -62: 112 type=126 (ANGLES) 58 60 62 -62: 113 type=127 (ANGLES) 61 60 62 -62: 114 type=116 (ANGLES) 60 62 63 -62: 115 type=116 (ANGLES) 60 62 64 -62: 116 type=129 (ANGLES) 60 62 65 -62: 117 type=121 (ANGLES) 63 62 64 -62: 118 type=116 (ANGLES) 63 62 65 -62: 119 type=116 (ANGLES) 64 62 65 -62: 120 type=122 (ANGLES) 62 65 66 -62: 121 type=123 (ANGLES) 62 65 67 -62: 122 type=124 (ANGLES) 66 65 67 -62: 123 type=125 (ANGLES) 65 67 68 -62: 124 type=126 (ANGLES) 65 67 69 -62: 125 type=127 (ANGLES) 68 67 69 -62: 126 type=116 (ANGLES) 67 69 70 -62: 127 type=128 (ANGLES) 67 69 71 -62: 128 type=129 (ANGLES) 67 69 89 -62: 129 type=118 (ANGLES) 70 69 71 -62: 130 type=116 (ANGLES) 70 69 89 -62: 131 type=119 (ANGLES) 71 69 89 -62: 132 type=118 (ANGLES) 69 71 72 -62: 133 type=118 (ANGLES) 69 71 73 -62: 134 type=120 (ANGLES) 69 71 74 -62: 135 type=121 (ANGLES) 72 71 73 -62: 136 type=118 (ANGLES) 72 71 74 -62: 137 type=118 (ANGLES) 73 71 74 -62: 138 type=118 (ANGLES) 71 74 75 -62: 139 type=118 (ANGLES) 71 74 76 -62: 140 type=120 (ANGLES) 71 74 77 -62: 141 type=121 (ANGLES) 75 74 76 -62: 142 type=118 (ANGLES) 75 74 77 -62: 143 type=118 (ANGLES) 76 74 77 -62: 144 type=118 (ANGLES) 74 77 78 -62: 145 type=118 (ANGLES) 74 77 79 -62: 146 type=117 (ANGLES) 74 77 80 -62: 147 type=121 (ANGLES) 78 77 79 -62: 148 type=116 (ANGLES) 78 77 80 -62: 149 type=116 (ANGLES) 79 77 80 -62: 150 type=134 (ANGLES) 77 80 81 -62: 151 type=135 (ANGLES) 77 80 82 -62: 152 type=133 (ANGLES) 81 80 82 -62: 153 type=131 (ANGLES) 80 82 83 -62: 154 type=131 (ANGLES) 80 82 86 -62: 155 type=131 (ANGLES) 83 82 86 -62: 156 type=133 (ANGLES) 82 83 84 -62: 157 type=133 (ANGLES) 82 83 85 -62: 158 type=133 (ANGLES) 84 83 85 -62: 159 type=133 (ANGLES) 82 86 87 -62: 160 type=133 (ANGLES) 82 86 88 -62: 161 type=133 (ANGLES) 87 86 88 -62: 162 type=122 (ANGLES) 69 89 90 -62: 163 type=123 (ANGLES) 69 89 91 -62: 164 type=124 (ANGLES) 90 89 91 -62: 165 type=125 (ANGLES) 89 91 92 -62: 166 type=126 (ANGLES) 89 91 93 -62: 167 type=127 (ANGLES) 92 91 93 -62: 168 type=116 (ANGLES) 91 93 94 -62: 169 type=128 (ANGLES) 91 93 95 -62: 170 type=129 (ANGLES) 91 93 100 -62: 171 type=118 (ANGLES) 94 93 95 -62: 172 type=116 (ANGLES) 94 93 100 -62: 173 type=119 (ANGLES) 95 93 100 -62: 174 type=118 (ANGLES) 93 95 96 -62: 175 type=118 (ANGLES) 93 95 97 -62: 176 type=136 (ANGLES) 93 95 98 -62: 177 type=121 (ANGLES) 96 95 97 -62: 178 type=116 (ANGLES) 96 95 98 -62: 179 type=116 (ANGLES) 97 95 98 -62: 180 type=137 (ANGLES) 95 98 99 -62: 181 type=122 (ANGLES) 93 100 101 -62: 182 type=123 (ANGLES) 93 100 102 -62: 183 type=124 (ANGLES) 101 100 102 -62: 184 type=125 (ANGLES) 100 102 103 -62: 185 type=126 (ANGLES) 100 102 104 -62: 186 type=127 (ANGLES) 103 102 104 -62: 187 type=116 (ANGLES) 102 104 105 -62: 188 type=128 (ANGLES) 102 104 106 -62: 189 type=129 (ANGLES) 102 104 115 -62: 190 type=118 (ANGLES) 105 104 106 -62: 191 type=116 (ANGLES) 105 104 115 -62: 192 type=119 (ANGLES) 106 104 115 -62: 193 type=118 (ANGLES) 104 106 107 -62: 194 type=118 (ANGLES) 104 106 108 -62: 195 type=120 (ANGLES) 104 106 109 -62: 196 type=121 (ANGLES) 107 106 108 -62: 197 type=118 (ANGLES) 107 106 109 -62: 198 type=118 (ANGLES) 108 106 109 -62: 199 type=118 (ANGLES) 106 109 110 -62: 200 type=118 (ANGLES) 106 109 111 -62: 201 type=119 (ANGLES) 106 109 112 -62: 202 type=121 (ANGLES) 110 109 111 -62: 203 type=116 (ANGLES) 110 109 112 -62: 204 type=116 (ANGLES) 111 109 112 -62: 205 type=138 (ANGLES) 109 112 113 -62: 206 type=138 (ANGLES) 109 112 114 -62: 207 type=139 (ANGLES) 113 112 114 -62: 208 type=122 (ANGLES) 104 115 116 -62: 209 type=123 (ANGLES) 104 115 117 -62: 210 type=124 (ANGLES) 116 115 117 -62: 211 type=125 (ANGLES) 115 117 118 -62: 212 type=126 (ANGLES) 115 117 119 -62: 213 type=127 (ANGLES) 118 117 119 -62: 214 type=116 (ANGLES) 117 119 120 -62: 215 type=128 (ANGLES) 117 119 121 -62: 216 type=129 (ANGLES) 117 119 134 -62: 217 type=118 (ANGLES) 120 119 121 -62: 218 type=116 (ANGLES) 120 119 134 -62: 219 type=119 (ANGLES) 121 119 134 -62: 220 type=118 (ANGLES) 119 121 122 -62: 221 type=118 (ANGLES) 119 121 123 -62: 222 type=120 (ANGLES) 119 121 124 -62: 223 type=121 (ANGLES) 122 121 123 -62: 224 type=118 (ANGLES) 122 121 124 -62: 225 type=118 (ANGLES) 123 121 124 -62: 226 type=118 (ANGLES) 121 124 125 -62: 227 type=120 (ANGLES) 121 124 126 -62: 228 type=120 (ANGLES) 121 124 130 -62: 229 type=118 (ANGLES) 125 124 126 -62: 230 type=118 (ANGLES) 125 124 130 -62: 231 type=120 (ANGLES) 126 124 130 -62: 232 type=118 (ANGLES) 124 126 127 -62: 233 type=118 (ANGLES) 124 126 128 -62: 234 type=118 (ANGLES) 124 126 129 -62: 235 type=121 (ANGLES) 127 126 128 -62: 236 type=121 (ANGLES) 127 126 129 -62: 237 type=121 (ANGLES) 128 126 129 -62: 238 type=118 (ANGLES) 124 130 131 -62: 239 type=118 (ANGLES) 124 130 132 -62: 240 type=118 (ANGLES) 124 130 133 -62: 241 type=121 (ANGLES) 131 130 132 -62: 242 type=121 (ANGLES) 131 130 133 -62: 243 type=121 (ANGLES) 132 130 133 -62: 244 type=122 (ANGLES) 119 134 135 -62: 245 type=123 (ANGLES) 119 134 136 -62: 246 type=124 (ANGLES) 135 134 136 -62: 247 type=125 (ANGLES) 134 136 137 -62: 248 type=126 (ANGLES) 134 136 138 -62: 249 type=127 (ANGLES) 137 136 138 -62: 250 type=116 (ANGLES) 136 138 139 -62: 251 type=128 (ANGLES) 136 138 140 -62: 252 type=129 (ANGLES) 136 138 144 -62: 253 type=118 (ANGLES) 139 138 140 -62: 254 type=116 (ANGLES) 139 138 144 -62: 255 type=119 (ANGLES) 140 138 144 -62: 256 type=118 (ANGLES) 138 140 141 -62: 257 type=118 (ANGLES) 138 140 142 -62: 258 type=118 (ANGLES) 138 140 143 -62: 259 type=121 (ANGLES) 141 140 142 -62: 260 type=121 (ANGLES) 141 140 143 -62: 261 type=121 (ANGLES) 142 140 143 -62: 262 type=122 (ANGLES) 138 144 145 -62: 263 type=123 (ANGLES) 138 144 146 -62: 264 type=124 (ANGLES) 145 144 146 -62: 265 type=125 (ANGLES) 144 146 147 -62: 266 type=126 (ANGLES) 144 146 148 -62: 267 type=127 (ANGLES) 147 146 148 -62: 268 type=116 (ANGLES) 146 148 149 -62: 269 type=128 (ANGLES) 146 148 150 -62: 270 type=129 (ANGLES) 146 148 154 -62: 271 type=118 (ANGLES) 149 148 150 -62: 272 type=116 (ANGLES) 149 148 154 -62: 273 type=119 (ANGLES) 150 148 154 -62: 274 type=118 (ANGLES) 148 150 151 -62: 275 type=118 (ANGLES) 148 150 152 -62: 276 type=118 (ANGLES) 148 150 153 -62: 277 type=121 (ANGLES) 151 150 152 -62: 278 type=121 (ANGLES) 151 150 153 -62: 279 type=121 (ANGLES) 152 150 153 -62: 280 type=122 (ANGLES) 148 154 155 -62: G96Angle: -62: nr: 0 -62: Restr. Angles: -62: nr: 0 -62: Lin. Angle: -62: nr: 0 -62: Bond-Cross: -62: nr: 0 -62: BA-Cross: -62: nr: 0 -62: U-B: -62: nr: 0 -62: Quartic Angles: -62: nr: 0 -62: Tab. Angles: -62: nr: 0 -62: Proper Dih.: -62: nr: 145 -62: iatoms: -62: 0 type=140 (PDIHS) 4 24 22 23 -62: 1 type=141 (PDIHS) 22 26 24 25 -62: 2 type=140 (PDIHS) 26 40 38 39 -62: 3 type=141 (PDIHS) 38 42 40 41 -62: 4 type=140 (PDIHS) 42 60 58 59 -62: 5 type=142 (PDIHS) 44 47 50 48 -62: 6 type=142 (PDIHS) 47 52 48 49 -62: 7 type=142 (PDIHS) 47 54 50 51 -62: 8 type=142 (PDIHS) 48 56 52 53 -62: 9 type=142 (PDIHS) 50 56 54 55 -62: 10 type=142 (PDIHS) 52 54 56 57 -62: 11 type=141 (PDIHS) 58 62 60 61 -62: 12 type=140 (PDIHS) 62 67 65 66 -62: 13 type=141 (PDIHS) 65 69 67 68 -62: 14 type=140 (PDIHS) 69 91 89 90 -62: 15 type=141 (PDIHS) 77 82 80 81 -62: 16 type=140 (PDIHS) 80 83 82 86 -62: 17 type=141 (PDIHS) 82 84 83 85 -62: 18 type=141 (PDIHS) 82 87 86 88 -62: 19 type=141 (PDIHS) 89 93 91 92 -62: 20 type=140 (PDIHS) 93 102 100 101 -62: 21 type=141 (PDIHS) 100 104 102 103 -62: 22 type=140 (PDIHS) 104 117 115 116 -62: 23 type=140 (PDIHS) 109 113 112 114 -62: 24 type=141 (PDIHS) 115 119 117 118 -62: 25 type=140 (PDIHS) 119 136 134 135 -62: 26 type=141 (PDIHS) 134 138 136 137 -62: 27 type=140 (PDIHS) 138 146 144 145 -62: 28 type=141 (PDIHS) 144 148 146 147 -62: Ryckaert-Bell.: -62: nr: 1565 -62: iatoms: -62: 0 type=143 (RBDIHS) 1 0 4 5 -62: 1 type=144 (RBDIHS) 1 0 4 6 -62: 2 type=144 (RBDIHS) 1 0 4 22 -62: 3 type=143 (RBDIHS) 2 0 4 5 -62: 4 type=144 (RBDIHS) 2 0 4 6 -62: 5 type=144 (RBDIHS) 2 0 4 22 -62: 6 type=143 (RBDIHS) 3 0 4 5 -62: 7 type=144 (RBDIHS) 3 0 4 6 -62: 8 type=144 (RBDIHS) 3 0 4 22 -62: 9 type=145 (RBDIHS) 0 4 6 9 -62: 10 type=146 (RBDIHS) 22 4 6 9 -62: 11 type=147 (RBDIHS) 0 4 6 7 -62: 12 type=147 (RBDIHS) 0 4 6 8 -62: 13 type=148 (RBDIHS) 5 4 6 7 -62: 14 type=148 (RBDIHS) 5 4 6 8 -62: 15 type=148 (RBDIHS) 5 4 6 9 -62: 16 type=149 (RBDIHS) 22 4 6 7 -62: 17 type=149 (RBDIHS) 22 4 6 8 -62: 18 type=150 (RBDIHS) 0 4 22 24 -62: 19 type=151 (RBDIHS) 6 4 22 24 -62: 20 type=148 (RBDIHS) 4 6 9 10 -62: 21 type=148 (RBDIHS) 4 6 9 11 -62: 22 type=152 (RBDIHS) 4 6 9 12 -62: 23 type=148 (RBDIHS) 7 6 9 10 -62: 24 type=148 (RBDIHS) 7 6 9 11 -62: 25 type=148 (RBDIHS) 7 6 9 12 -62: 26 type=148 (RBDIHS) 8 6 9 10 -62: 27 type=148 (RBDIHS) 8 6 9 11 -62: 28 type=148 (RBDIHS) 8 6 9 12 -62: 29 type=148 (RBDIHS) 6 9 12 13 -62: 30 type=148 (RBDIHS) 6 9 12 14 -62: 31 type=152 (RBDIHS) 6 9 12 15 -62: 32 type=148 (RBDIHS) 10 9 12 13 -62: 33 type=148 (RBDIHS) 10 9 12 14 -62: 34 type=148 (RBDIHS) 10 9 12 15 -62: 35 type=148 (RBDIHS) 11 9 12 13 -62: 36 type=148 (RBDIHS) 11 9 12 14 -62: 37 type=148 (RBDIHS) 11 9 12 15 -62: 38 type=148 (RBDIHS) 9 12 15 16 -62: 39 type=148 (RBDIHS) 9 12 15 17 -62: 40 type=153 (RBDIHS) 9 12 15 18 -62: 41 type=148 (RBDIHS) 13 12 15 16 -62: 42 type=148 (RBDIHS) 13 12 15 17 -62: 43 type=154 (RBDIHS) 13 12 15 18 -62: 44 type=148 (RBDIHS) 14 12 15 16 -62: 45 type=148 (RBDIHS) 14 12 15 17 -62: 46 type=154 (RBDIHS) 14 12 15 18 -62: 47 type=144 (RBDIHS) 12 15 18 19 -62: 48 type=144 (RBDIHS) 12 15 18 20 -62: 49 type=144 (RBDIHS) 12 15 18 21 -62: 50 type=143 (RBDIHS) 16 15 18 19 -62: 51 type=143 (RBDIHS) 16 15 18 20 -62: 52 type=143 (RBDIHS) 16 15 18 21 -62: 53 type=143 (RBDIHS) 17 15 18 19 -62: 54 type=143 (RBDIHS) 17 15 18 20 -62: 55 type=143 (RBDIHS) 17 15 18 21 -62: 56 type=155 (RBDIHS) 4 22 24 25 -62: 57 type=156 (RBDIHS) 4 22 24 26 -62: 58 type=155 (RBDIHS) 23 22 24 25 -62: 59 type=157 (RBDIHS) 23 22 24 26 -62: 60 type=158 (RBDIHS) 22 24 26 28 -62: 61 type=159 (RBDIHS) 22 24 26 38 -62: 62 type=160 (RBDIHS) 24 26 28 30 -62: 63 type=160 (RBDIHS) 24 26 28 34 -62: 64 type=161 (RBDIHS) 38 26 28 30 -62: 65 type=161 (RBDIHS) 38 26 28 34 -62: 66 type=147 (RBDIHS) 24 26 28 29 -62: 67 type=148 (RBDIHS) 27 26 28 29 -62: 68 type=148 (RBDIHS) 27 26 28 30 -62: 69 type=148 (RBDIHS) 27 26 28 34 -62: 70 type=149 (RBDIHS) 38 26 28 29 -62: 71 type=150 (RBDIHS) 24 26 38 40 -62: 72 type=151 (RBDIHS) 28 26 38 40 -62: 73 type=148 (RBDIHS) 26 28 30 31 -62: 74 type=148 (RBDIHS) 26 28 30 32 -62: 75 type=148 (RBDIHS) 26 28 30 33 -62: 76 type=148 (RBDIHS) 29 28 30 31 -62: 77 type=148 (RBDIHS) 29 28 30 32 -62: 78 type=148 (RBDIHS) 29 28 30 33 -62: 79 type=148 (RBDIHS) 34 28 30 31 -62: 80 type=148 (RBDIHS) 34 28 30 32 -62: 81 type=148 (RBDIHS) 34 28 30 33 -62: 82 type=148 (RBDIHS) 26 28 34 35 -62: 83 type=148 (RBDIHS) 26 28 34 36 -62: 84 type=148 (RBDIHS) 26 28 34 37 -62: 85 type=148 (RBDIHS) 29 28 34 35 -62: 86 type=148 (RBDIHS) 29 28 34 36 -62: 87 type=148 (RBDIHS) 29 28 34 37 -62: 88 type=148 (RBDIHS) 30 28 34 35 -62: 89 type=148 (RBDIHS) 30 28 34 36 -62: 90 type=148 (RBDIHS) 30 28 34 37 -62: 91 type=155 (RBDIHS) 26 38 40 41 -62: 92 type=156 (RBDIHS) 26 38 40 42 -62: 93 type=155 (RBDIHS) 39 38 40 41 -62: 94 type=157 (RBDIHS) 39 38 40 42 -62: 95 type=158 (RBDIHS) 38 40 42 44 -62: 96 type=159 (RBDIHS) 38 40 42 58 -62: 97 type=147 (RBDIHS) 40 42 44 45 -62: 98 type=147 (RBDIHS) 40 42 44 46 -62: 99 type=162 (RBDIHS) 40 42 44 47 -62: 100 type=148 (RBDIHS) 43 42 44 45 -62: 101 type=148 (RBDIHS) 43 42 44 46 -62: 102 type=163 (RBDIHS) 43 42 44 47 -62: 103 type=149 (RBDIHS) 58 42 44 45 -62: 104 type=149 (RBDIHS) 58 42 44 46 -62: 105 type=164 (RBDIHS) 58 42 44 47 -62: 106 type=150 (RBDIHS) 40 42 58 60 -62: 107 type=151 (RBDIHS) 44 42 58 60 -62: 108 type=165 (RBDIHS) 44 47 48 49 -62: 109 type=165 (RBDIHS) 44 47 48 52 -62: 110 type=165 (RBDIHS) 50 47 48 49 -62: 111 type=165 (RBDIHS) 50 47 48 52 -62: 112 type=165 (RBDIHS) 44 47 50 51 -62: 113 type=165 (RBDIHS) 44 47 50 54 -62: 114 type=165 (RBDIHS) 48 47 50 51 -62: 115 type=165 (RBDIHS) 48 47 50 54 -62: 116 type=165 (RBDIHS) 47 48 52 53 -62: 117 type=165 (RBDIHS) 47 48 52 56 -62: 118 type=165 (RBDIHS) 49 48 52 53 -62: 119 type=165 (RBDIHS) 49 48 52 56 -62: 120 type=165 (RBDIHS) 47 50 54 55 -62: 121 type=165 (RBDIHS) 47 50 54 56 -62: 122 type=165 (RBDIHS) 51 50 54 55 -62: 123 type=165 (RBDIHS) 51 50 54 56 -62: 124 type=165 (RBDIHS) 48 52 56 54 -62: 125 type=165 (RBDIHS) 48 52 56 57 -62: 126 type=165 (RBDIHS) 53 52 56 54 -62: 127 type=165 (RBDIHS) 53 52 56 57 -62: 128 type=165 (RBDIHS) 50 54 56 52 -62: 129 type=165 (RBDIHS) 50 54 56 57 -62: 130 type=165 (RBDIHS) 55 54 56 52 -62: 131 type=165 (RBDIHS) 55 54 56 57 -62: 132 type=155 (RBDIHS) 42 58 60 61 -62: 133 type=156 (RBDIHS) 42 58 60 62 -62: 134 type=155 (RBDIHS) 59 58 60 61 -62: 135 type=157 (RBDIHS) 59 58 60 62 -62: 136 type=159 (RBDIHS) 58 60 62 65 -62: 137 type=150 (RBDIHS) 60 62 65 67 -62: 138 type=155 (RBDIHS) 62 65 67 68 -62: 139 type=156 (RBDIHS) 62 65 67 69 -62: 140 type=155 (RBDIHS) 66 65 67 68 -62: 141 type=157 (RBDIHS) 66 65 67 69 -62: 142 type=158 (RBDIHS) 65 67 69 71 -62: 143 type=159 (RBDIHS) 65 67 69 89 -62: 144 type=166 (RBDIHS) 67 69 71 74 -62: 145 type=167 (RBDIHS) 89 69 71 74 -62: 146 type=147 (RBDIHS) 67 69 71 72 -62: 147 type=147 (RBDIHS) 67 69 71 73 -62: 148 type=148 (RBDIHS) 70 69 71 72 -62: 149 type=148 (RBDIHS) 70 69 71 73 -62: 150 type=148 (RBDIHS) 70 69 71 74 -62: 151 type=149 (RBDIHS) 89 69 71 72 -62: 152 type=149 (RBDIHS) 89 69 71 73 -62: 153 type=150 (RBDIHS) 67 69 89 91 -62: 154 type=151 (RBDIHS) 71 69 89 91 -62: 155 type=148 (RBDIHS) 69 71 74 75 -62: 156 type=148 (RBDIHS) 69 71 74 76 -62: 157 type=152 (RBDIHS) 69 71 74 77 -62: 158 type=148 (RBDIHS) 72 71 74 75 -62: 159 type=148 (RBDIHS) 72 71 74 76 -62: 160 type=148 (RBDIHS) 72 71 74 77 -62: 161 type=148 (RBDIHS) 73 71 74 75 -62: 162 type=148 (RBDIHS) 73 71 74 76 -62: 163 type=148 (RBDIHS) 73 71 74 77 -62: 164 type=148 (RBDIHS) 71 74 77 78 -62: 165 type=148 (RBDIHS) 71 74 77 79 -62: 166 type=153 (RBDIHS) 71 74 77 80 -62: 167 type=148 (RBDIHS) 75 74 77 78 -62: 168 type=148 (RBDIHS) 75 74 77 79 -62: 169 type=168 (RBDIHS) 75 74 77 80 -62: 170 type=148 (RBDIHS) 76 74 77 78 -62: 171 type=148 (RBDIHS) 76 74 77 79 -62: 172 type=168 (RBDIHS) 76 74 77 80 -62: 173 type=169 (RBDIHS) 74 77 80 81 -62: 174 type=170 (RBDIHS) 74 77 80 82 -62: 175 type=171 (RBDIHS) 78 77 80 82 -62: 176 type=171 (RBDIHS) 79 77 80 82 -62: 177 type=172 (RBDIHS) 77 80 82 83 -62: 178 type=172 (RBDIHS) 77 80 82 86 -62: 179 type=173 (RBDIHS) 81 80 82 83 -62: 180 type=173 (RBDIHS) 81 80 82 86 -62: 181 type=173 (RBDIHS) 80 82 83 84 -62: 182 type=173 (RBDIHS) 80 82 83 85 -62: 183 type=173 (RBDIHS) 86 82 83 84 -62: 184 type=173 (RBDIHS) 86 82 83 85 -62: 185 type=173 (RBDIHS) 80 82 86 87 -62: 186 type=173 (RBDIHS) 80 82 86 88 -62: 187 type=173 (RBDIHS) 83 82 86 87 -62: 188 type=173 (RBDIHS) 83 82 86 88 -62: 189 type=155 (RBDIHS) 69 89 91 92 -62: 190 type=156 (RBDIHS) 69 89 91 93 -62: 191 type=155 (RBDIHS) 90 89 91 92 -62: 192 type=157 (RBDIHS) 90 89 91 93 -62: 193 type=158 (RBDIHS) 89 91 93 95 -62: 194 type=159 (RBDIHS) 89 91 93 100 -62: 195 type=174 (RBDIHS) 91 93 95 98 -62: 196 type=175 (RBDIHS) 100 93 95 98 -62: 197 type=147 (RBDIHS) 91 93 95 96 -62: 198 type=147 (RBDIHS) 91 93 95 97 -62: 199 type=148 (RBDIHS) 94 93 95 96 -62: 200 type=148 (RBDIHS) 94 93 95 97 -62: 201 type=176 (RBDIHS) 94 93 95 98 -62: 202 type=149 (RBDIHS) 100 93 95 96 -62: 203 type=149 (RBDIHS) 100 93 95 97 -62: 204 type=150 (RBDIHS) 91 93 100 102 -62: 205 type=151 (RBDIHS) 95 93 100 102 -62: 206 type=177 (RBDIHS) 93 95 98 99 -62: 207 type=178 (RBDIHS) 96 95 98 99 -62: 208 type=178 (RBDIHS) 97 95 98 99 -62: 209 type=155 (RBDIHS) 93 100 102 103 -62: 210 type=156 (RBDIHS) 93 100 102 104 -62: 211 type=155 (RBDIHS) 101 100 102 103 -62: 212 type=157 (RBDIHS) 101 100 102 104 -62: 213 type=158 (RBDIHS) 100 102 104 106 -62: 214 type=159 (RBDIHS) 100 102 104 115 -62: 215 type=179 (RBDIHS) 102 104 106 109 -62: 216 type=180 (RBDIHS) 115 104 106 109 -62: 217 type=147 (RBDIHS) 102 104 106 107 -62: 218 type=147 (RBDIHS) 102 104 106 108 -62: 219 type=148 (RBDIHS) 105 104 106 107 -62: 220 type=148 (RBDIHS) 105 104 106 108 -62: 221 type=148 (RBDIHS) 105 104 106 109 -62: 222 type=149 (RBDIHS) 115 104 106 107 -62: 223 type=149 (RBDIHS) 115 104 106 108 -62: 224 type=150 (RBDIHS) 102 104 115 117 -62: 225 type=151 (RBDIHS) 106 104 115 117 -62: 226 type=148 (RBDIHS) 104 106 109 110 -62: 227 type=148 (RBDIHS) 104 106 109 111 -62: 228 type=181 (RBDIHS) 104 106 109 112 -62: 229 type=148 (RBDIHS) 107 106 109 110 -62: 230 type=148 (RBDIHS) 107 106 109 111 -62: 231 type=182 (RBDIHS) 107 106 109 112 -62: 232 type=148 (RBDIHS) 108 106 109 110 -62: 233 type=148 (RBDIHS) 108 106 109 111 -62: 234 type=182 (RBDIHS) 108 106 109 112 -62: 235 type=183 (RBDIHS) 106 109 112 113 -62: 236 type=183 (RBDIHS) 106 109 112 114 -62: 237 type=155 (RBDIHS) 104 115 117 118 -62: 238 type=156 (RBDIHS) 104 115 117 119 -62: 239 type=155 (RBDIHS) 116 115 117 118 -62: 240 type=157 (RBDIHS) 116 115 117 119 -62: 241 type=158 (RBDIHS) 115 117 119 121 -62: 242 type=159 (RBDIHS) 115 117 119 134 -62: 243 type=184 (RBDIHS) 117 119 121 124 -62: 244 type=185 (RBDIHS) 134 119 121 124 -62: 245 type=147 (RBDIHS) 117 119 121 122 -62: 246 type=147 (RBDIHS) 117 119 121 123 -62: 247 type=148 (RBDIHS) 120 119 121 122 -62: 248 type=148 (RBDIHS) 120 119 121 123 -62: 249 type=148 (RBDIHS) 120 119 121 124 -62: 250 type=149 (RBDIHS) 134 119 121 122 -62: 251 type=149 (RBDIHS) 134 119 121 123 -62: 252 type=150 (RBDIHS) 117 119 134 136 -62: 253 type=151 (RBDIHS) 121 119 134 136 -62: 254 type=148 (RBDIHS) 119 121 124 125 -62: 255 type=152 (RBDIHS) 119 121 124 126 -62: 256 type=152 (RBDIHS) 119 121 124 130 -62: 257 type=148 (RBDIHS) 122 121 124 125 -62: 258 type=148 (RBDIHS) 122 121 124 126 -62: 259 type=148 (RBDIHS) 122 121 124 130 -62: 260 type=148 (RBDIHS) 123 121 124 125 -62: 261 type=148 (RBDIHS) 123 121 124 126 -62: 262 type=148 (RBDIHS) 123 121 124 130 -62: 263 type=148 (RBDIHS) 121 124 126 127 -62: 264 type=148 (RBDIHS) 121 124 126 128 -62: 265 type=148 (RBDIHS) 121 124 126 129 -62: 266 type=148 (RBDIHS) 125 124 126 127 -62: 267 type=148 (RBDIHS) 125 124 126 128 -62: 268 type=148 (RBDIHS) 125 124 126 129 -62: 269 type=148 (RBDIHS) 130 124 126 127 -62: 270 type=148 (RBDIHS) 130 124 126 128 -62: 271 type=148 (RBDIHS) 130 124 126 129 -62: 272 type=148 (RBDIHS) 121 124 130 131 -62: 273 type=148 (RBDIHS) 121 124 130 132 -62: 274 type=148 (RBDIHS) 121 124 130 133 -62: 275 type=148 (RBDIHS) 125 124 130 131 -62: 276 type=148 (RBDIHS) 125 124 130 132 -62: 277 type=148 (RBDIHS) 125 124 130 133 -62: 278 type=148 (RBDIHS) 126 124 130 131 -62: 279 type=148 (RBDIHS) 126 124 130 132 -62: 280 type=148 (RBDIHS) 126 124 130 133 -62: 281 type=155 (RBDIHS) 119 134 136 137 -62: 282 type=156 (RBDIHS) 119 134 136 138 -62: 283 type=155 (RBDIHS) 135 134 136 137 -62: 284 type=157 (RBDIHS) 135 134 136 138 -62: 285 type=158 (RBDIHS) 134 136 138 140 -62: 286 type=159 (RBDIHS) 134 136 138 144 -62: 287 type=147 (RBDIHS) 136 138 140 141 -62: 288 type=147 (RBDIHS) 136 138 140 142 -62: 289 type=147 (RBDIHS) 136 138 140 143 -62: 290 type=148 (RBDIHS) 139 138 140 141 -62: 291 type=148 (RBDIHS) 139 138 140 142 -62: 292 type=148 (RBDIHS) 139 138 140 143 -62: 293 type=149 (RBDIHS) 144 138 140 141 -62: 294 type=149 (RBDIHS) 144 138 140 142 -62: 295 type=149 (RBDIHS) 144 138 140 143 -62: 296 type=150 (RBDIHS) 136 138 144 146 -62: 297 type=151 (RBDIHS) 140 138 144 146 -62: 298 type=155 (RBDIHS) 138 144 146 147 -62: 299 type=156 (RBDIHS) 138 144 146 148 -62: 300 type=155 (RBDIHS) 145 144 146 147 -62: 301 type=157 (RBDIHS) 145 144 146 148 -62: 302 type=158 (RBDIHS) 144 146 148 150 -62: 303 type=159 (RBDIHS) 144 146 148 154 -62: 304 type=147 (RBDIHS) 146 148 150 151 -62: 305 type=147 (RBDIHS) 146 148 150 152 -62: 306 type=147 (RBDIHS) 146 148 150 153 -62: 307 type=148 (RBDIHS) 149 148 150 151 -62: 308 type=148 (RBDIHS) 149 148 150 152 -62: 309 type=148 (RBDIHS) 149 148 150 153 -62: 310 type=149 (RBDIHS) 154 148 150 151 -62: 311 type=149 (RBDIHS) 154 148 150 152 -62: 312 type=149 (RBDIHS) 154 148 150 153 -62: Restr. Dih.: -62: nr: 0 -62: CBT Dih.: -62: nr: 0 -62: Fourier Dih.: -62: nr: 0 -62: Improper Dih.: -62: nr: 0 -62: Per. Imp. Dih.: -62: nr: 0 -62: Tab. Dih.: -62: nr: 0 -62: CMAP Dih.: -62: nr: 0 -62: GB 1-2 Pol.: -62: nr: 0 -62: GB 1-3 Pol.: -62: nr: 0 -62: GB 1-4 Pol.: -62: nr: 0 -62: GB Polariz.: -62: nr: 0 -62: Nonpolar Sol.: -62: nr: 0 -62: LJ-14: -62: nr: 1197 -62: iatoms: -62: 0 type=186 (LJ14) 0 7 -62: 1 type=186 (LJ14) 0 8 -62: 2 type=187 (LJ14) 0 9 -62: 3 type=188 (LJ14) 0 23 -62: 4 type=189 (LJ14) 0 24 -62: 5 type=190 (LJ14) 1 5 -62: 6 type=190 (LJ14) 1 6 -62: 7 type=190 (LJ14) 1 22 -62: 8 type=190 (LJ14) 2 5 -62: 9 type=190 (LJ14) 2 6 -62: 10 type=190 (LJ14) 2 22 -62: 11 type=190 (LJ14) 3 5 -62: 12 type=190 (LJ14) 3 6 -62: 13 type=190 (LJ14) 3 22 -62: 14 type=191 (LJ14) 4 10 -62: 15 type=191 (LJ14) 4 11 -62: 16 type=192 (LJ14) 4 12 -62: 17 type=190 (LJ14) 4 25 -62: 18 type=192 (LJ14) 4 26 -62: 19 type=193 (LJ14) 5 7 -62: 20 type=193 (LJ14) 5 8 -62: 21 type=191 (LJ14) 5 9 -62: 22 type=194 (LJ14) 5 23 -62: 23 type=186 (LJ14) 5 24 -62: 24 type=191 (LJ14) 6 13 -62: 25 type=191 (LJ14) 6 14 -62: 26 type=192 (LJ14) 6 15 -62: 27 type=195 (LJ14) 6 23 -62: 28 type=187 (LJ14) 6 24 -62: 29 type=193 (LJ14) 7 10 -62: 30 type=193 (LJ14) 7 11 -62: 31 type=191 (LJ14) 7 12 -62: 32 type=196 (LJ14) 7 22 -62: 33 type=193 (LJ14) 8 10 -62: 34 type=193 (LJ14) 8 11 -62: 35 type=191 (LJ14) 8 12 -62: 36 type=196 (LJ14) 8 22 -62: 37 type=191 (LJ14) 9 16 -62: 38 type=191 (LJ14) 9 17 -62: 39 type=187 (LJ14) 9 18 -62: 40 type=197 (LJ14) 9 22 -62: 41 type=193 (LJ14) 10 13 -62: 42 type=193 (LJ14) 10 14 -62: 43 type=191 (LJ14) 10 15 -62: 44 type=193 (LJ14) 11 13 -62: 45 type=193 (LJ14) 11 14 -62: 46 type=191 (LJ14) 11 15 -62: 47 type=190 (LJ14) 12 19 -62: 48 type=190 (LJ14) 12 20 -62: 49 type=190 (LJ14) 12 21 -62: 50 type=193 (LJ14) 13 16 -62: 51 type=193 (LJ14) 13 17 -62: 52 type=186 (LJ14) 13 18 -62: 53 type=193 (LJ14) 14 16 -62: 54 type=193 (LJ14) 14 17 -62: 55 type=186 (LJ14) 14 18 -62: 56 type=190 (LJ14) 16 19 -62: 57 type=190 (LJ14) 16 20 -62: 58 type=190 (LJ14) 16 21 -62: 59 type=190 (LJ14) 17 19 -62: 60 type=190 (LJ14) 17 20 -62: 61 type=190 (LJ14) 17 21 -62: 62 type=196 (LJ14) 22 27 -62: 63 type=197 (LJ14) 22 28 -62: 64 type=198 (LJ14) 22 38 -62: 65 type=190 (LJ14) 23 25 -62: 66 type=195 (LJ14) 23 26 -62: 67 type=186 (LJ14) 24 29 -62: 68 type=187 (LJ14) 24 30 -62: 69 type=187 (LJ14) 24 34 -62: 70 type=188 (LJ14) 24 39 -62: 71 type=189 (LJ14) 24 40 -62: 72 type=190 (LJ14) 25 27 -62: 73 type=190 (LJ14) 25 28 -62: 74 type=190 (LJ14) 25 38 -62: 75 type=191 (LJ14) 26 31 -62: 76 type=191 (LJ14) 26 32 -62: 77 type=191 (LJ14) 26 33 -62: 78 type=191 (LJ14) 26 35 -62: 79 type=191 (LJ14) 26 36 -62: 80 type=191 (LJ14) 26 37 -62: 81 type=190 (LJ14) 26 41 -62: 82 type=192 (LJ14) 26 42 -62: 83 type=193 (LJ14) 27 29 -62: 84 type=191 (LJ14) 27 30 -62: 85 type=191 (LJ14) 27 34 -62: 86 type=194 (LJ14) 27 39 -62: 87 type=186 (LJ14) 27 40 -62: 88 type=195 (LJ14) 28 39 -62: 89 type=187 (LJ14) 28 40 -62: 90 type=193 (LJ14) 29 31 -62: 91 type=193 (LJ14) 29 32 -62: 92 type=193 (LJ14) 29 33 -62: 93 type=193 (LJ14) 29 35 -62: 94 type=193 (LJ14) 29 36 -62: 95 type=193 (LJ14) 29 37 -62: 96 type=196 (LJ14) 29 38 -62: 97 type=191 (LJ14) 30 35 -62: 98 type=191 (LJ14) 30 36 -62: 99 type=191 (LJ14) 30 37 -62: 100 type=197 (LJ14) 30 38 -62: 101 type=191 (LJ14) 31 34 -62: 102 type=191 (LJ14) 32 34 -62: 103 type=191 (LJ14) 33 34 -62: 104 type=197 (LJ14) 34 38 -62: 105 type=196 (LJ14) 38 43 -62: 106 type=197 (LJ14) 38 44 -62: 107 type=198 (LJ14) 38 58 -62: 108 type=190 (LJ14) 39 41 -62: 109 type=195 (LJ14) 39 42 -62: 110 type=186 (LJ14) 40 45 -62: 111 type=186 (LJ14) 40 46 -62: 112 type=199 (LJ14) 40 47 -62: 113 type=188 (LJ14) 40 59 -62: 114 type=189 (LJ14) 40 60 -62: 115 type=190 (LJ14) 41 43 -62: 116 type=190 (LJ14) 41 44 -62: 117 type=190 (LJ14) 41 58 -62: 118 type=200 (LJ14) 42 48 -62: 119 type=200 (LJ14) 42 50 -62: 120 type=190 (LJ14) 42 61 -62: 121 type=192 (LJ14) 42 62 -62: 122 type=193 (LJ14) 43 45 -62: 123 type=193 (LJ14) 43 46 -62: 124 type=201 (LJ14) 43 47 -62: 125 type=194 (LJ14) 43 59 -62: 126 type=186 (LJ14) 43 60 -62: 127 type=202 (LJ14) 44 49 -62: 128 type=202 (LJ14) 44 51 -62: 129 type=200 (LJ14) 44 52 -62: 130 type=200 (LJ14) 44 54 -62: 131 type=195 (LJ14) 44 59 -62: 132 type=187 (LJ14) 44 60 -62: 133 type=201 (LJ14) 45 48 -62: 134 type=201 (LJ14) 45 50 -62: 135 type=196 (LJ14) 45 58 -62: 136 type=201 (LJ14) 46 48 -62: 137 type=201 (LJ14) 46 50 -62: 138 type=196 (LJ14) 46 58 -62: 139 type=203 (LJ14) 47 53 -62: 140 type=203 (LJ14) 47 55 -62: 141 type=204 (LJ14) 47 56 -62: 142 type=205 (LJ14) 47 58 -62: 143 type=203 (LJ14) 48 51 -62: 144 type=204 (LJ14) 48 54 -62: 145 type=203 (LJ14) 48 57 -62: 146 type=203 (LJ14) 49 50 -62: 147 type=206 (LJ14) 49 53 -62: 148 type=203 (LJ14) 49 56 -62: 149 type=204 (LJ14) 50 52 -62: 150 type=203 (LJ14) 50 57 -62: 151 type=206 (LJ14) 51 55 -62: 152 type=203 (LJ14) 51 56 -62: 153 type=203 (LJ14) 52 55 -62: 154 type=203 (LJ14) 53 54 -62: 155 type=206 (LJ14) 53 57 -62: 156 type=206 (LJ14) 55 57 -62: 157 type=196 (LJ14) 58 63 -62: 158 type=196 (LJ14) 58 64 -62: 159 type=198 (LJ14) 58 65 -62: 160 type=190 (LJ14) 59 61 -62: 161 type=195 (LJ14) 59 62 -62: 162 type=188 (LJ14) 60 66 -62: 163 type=189 (LJ14) 60 67 -62: 164 type=190 (LJ14) 61 63 -62: 165 type=190 (LJ14) 61 64 -62: 166 type=190 (LJ14) 61 65 -62: 167 type=190 (LJ14) 62 68 -62: 168 type=192 (LJ14) 62 69 -62: 169 type=194 (LJ14) 63 66 -62: 170 type=186 (LJ14) 63 67 -62: 171 type=194 (LJ14) 64 66 -62: 172 type=186 (LJ14) 64 67 -62: 173 type=196 (LJ14) 65 70 -62: 174 type=197 (LJ14) 65 71 -62: 175 type=198 (LJ14) 65 89 -62: 176 type=190 (LJ14) 66 68 -62: 177 type=195 (LJ14) 66 69 -62: 178 type=186 (LJ14) 67 72 -62: 179 type=186 (LJ14) 67 73 -62: 180 type=187 (LJ14) 67 74 -62: 181 type=188 (LJ14) 67 90 -62: 182 type=189 (LJ14) 67 91 -62: 183 type=190 (LJ14) 68 70 -62: 184 type=190 (LJ14) 68 71 -62: 185 type=190 (LJ14) 68 89 -62: 186 type=191 (LJ14) 69 75 -62: 187 type=191 (LJ14) 69 76 -62: 188 type=192 (LJ14) 69 77 -62: 189 type=190 (LJ14) 69 92 -62: 190 type=192 (LJ14) 69 93 -62: 191 type=193 (LJ14) 70 72 -62: 192 type=193 (LJ14) 70 73 -62: 193 type=191 (LJ14) 70 74 -62: 194 type=194 (LJ14) 70 90 -62: 195 type=186 (LJ14) 70 91 -62: 196 type=191 (LJ14) 71 78 -62: 197 type=191 (LJ14) 71 79 -62: 198 type=187 (LJ14) 71 80 -62: 199 type=195 (LJ14) 71 90 -62: 200 type=187 (LJ14) 71 91 -62: 201 type=193 (LJ14) 72 75 -62: 202 type=193 (LJ14) 72 76 -62: 203 type=191 (LJ14) 72 77 -62: 204 type=196 (LJ14) 72 89 -62: 205 type=193 (LJ14) 73 75 -62: 206 type=193 (LJ14) 73 76 -62: 207 type=191 (LJ14) 73 77 -62: 208 type=196 (LJ14) 73 89 -62: 209 type=190 (LJ14) 74 81 -62: 210 type=207 (LJ14) 74 82 -62: 211 type=197 (LJ14) 74 89 -62: 212 type=193 (LJ14) 75 78 -62: 213 type=193 (LJ14) 75 79 -62: 214 type=186 (LJ14) 75 80 -62: 215 type=193 (LJ14) 76 78 -62: 216 type=193 (LJ14) 76 79 -62: 217 type=186 (LJ14) 76 80 -62: 218 type=187 (LJ14) 77 83 -62: 219 type=187 (LJ14) 77 86 -62: 220 type=190 (LJ14) 78 81 -62: 221 type=208 (LJ14) 78 82 -62: 222 type=190 (LJ14) 79 81 -62: 223 type=208 (LJ14) 79 82 -62: 224 type=190 (LJ14) 80 84 -62: 225 type=190 (LJ14) 80 85 -62: 226 type=190 (LJ14) 80 87 -62: 227 type=190 (LJ14) 80 88 -62: 228 type=190 (LJ14) 81 83 -62: 229 type=190 (LJ14) 81 86 -62: 230 type=190 (LJ14) 83 87 -62: 231 type=190 (LJ14) 83 88 -62: 232 type=190 (LJ14) 84 86 -62: 233 type=190 (LJ14) 85 86 -62: 234 type=196 (LJ14) 89 94 -62: 235 type=197 (LJ14) 89 95 -62: 236 type=198 (LJ14) 89 100 -62: 237 type=190 (LJ14) 90 92 -62: 238 type=195 (LJ14) 90 93 -62: 239 type=186 (LJ14) 91 96 -62: 240 type=186 (LJ14) 91 97 -62: 241 type=209 (LJ14) 91 98 -62: 242 type=188 (LJ14) 91 101 -62: 243 type=189 (LJ14) 91 102 -62: 244 type=190 (LJ14) 92 94 -62: 245 type=190 (LJ14) 92 95 -62: 246 type=190 (LJ14) 92 100 -62: 247 type=190 (LJ14) 93 99 -62: 248 type=190 (LJ14) 93 103 -62: 249 type=192 (LJ14) 93 104 -62: 250 type=193 (LJ14) 94 96 -62: 251 type=193 (LJ14) 94 97 -62: 252 type=210 (LJ14) 94 98 -62: 253 type=194 (LJ14) 94 101 -62: 254 type=186 (LJ14) 94 102 -62: 255 type=195 (LJ14) 95 101 -62: 256 type=187 (LJ14) 95 102 -62: 257 type=190 (LJ14) 96 99 -62: 258 type=196 (LJ14) 96 100 -62: 259 type=190 (LJ14) 97 99 -62: 260 type=196 (LJ14) 97 100 -62: 261 type=211 (LJ14) 98 100 -62: 262 type=196 (LJ14) 100 105 -62: 263 type=197 (LJ14) 100 106 -62: 264 type=198 (LJ14) 100 115 -62: 265 type=190 (LJ14) 101 103 -62: 266 type=195 (LJ14) 101 104 -62: 267 type=186 (LJ14) 102 107 -62: 268 type=186 (LJ14) 102 108 -62: 269 type=187 (LJ14) 102 109 -62: 270 type=188 (LJ14) 102 116 -62: 271 type=189 (LJ14) 102 117 -62: 272 type=190 (LJ14) 103 105 -62: 273 type=190 (LJ14) 103 106 -62: 274 type=190 (LJ14) 103 115 -62: 275 type=191 (LJ14) 104 110 -62: 276 type=191 (LJ14) 104 111 -62: 277 type=197 (LJ14) 104 112 -62: 278 type=190 (LJ14) 104 118 -62: 279 type=192 (LJ14) 104 119 -62: 280 type=193 (LJ14) 105 107 -62: 281 type=193 (LJ14) 105 108 -62: 282 type=191 (LJ14) 105 109 -62: 283 type=194 (LJ14) 105 116 -62: 284 type=186 (LJ14) 105 117 -62: 285 type=195 (LJ14) 106 113 -62: 286 type=195 (LJ14) 106 114 -62: 287 type=195 (LJ14) 106 116 -62: 288 type=187 (LJ14) 106 117 -62: 289 type=193 (LJ14) 107 110 -62: 290 type=193 (LJ14) 107 111 -62: 291 type=196 (LJ14) 107 112 -62: 292 type=196 (LJ14) 107 115 -62: 293 type=193 (LJ14) 108 110 -62: 294 type=193 (LJ14) 108 111 -62: 295 type=196 (LJ14) 108 112 -62: 296 type=196 (LJ14) 108 115 -62: 297 type=197 (LJ14) 109 115 -62: 298 type=194 (LJ14) 110 113 -62: 299 type=194 (LJ14) 110 114 -62: 300 type=194 (LJ14) 111 113 -62: 301 type=194 (LJ14) 111 114 -62: 302 type=196 (LJ14) 115 120 -62: 303 type=197 (LJ14) 115 121 -62: 304 type=198 (LJ14) 115 134 -62: 305 type=190 (LJ14) 116 118 -62: 306 type=195 (LJ14) 116 119 -62: 307 type=186 (LJ14) 117 122 -62: 308 type=186 (LJ14) 117 123 -62: 309 type=187 (LJ14) 117 124 -62: 310 type=188 (LJ14) 117 135 -62: 311 type=189 (LJ14) 117 136 -62: 312 type=190 (LJ14) 118 120 -62: 313 type=190 (LJ14) 118 121 -62: 314 type=190 (LJ14) 118 134 -62: 315 type=191 (LJ14) 119 125 -62: 316 type=192 (LJ14) 119 126 -62: 317 type=192 (LJ14) 119 130 -62: 318 type=190 (LJ14) 119 137 -62: 319 type=192 (LJ14) 119 138 -62: 320 type=193 (LJ14) 120 122 -62: 321 type=193 (LJ14) 120 123 -62: 322 type=191 (LJ14) 120 124 -62: 323 type=194 (LJ14) 120 135 -62: 324 type=186 (LJ14) 120 136 -62: 325 type=191 (LJ14) 121 127 -62: 326 type=191 (LJ14) 121 128 -62: 327 type=191 (LJ14) 121 129 -62: 328 type=191 (LJ14) 121 131 -62: 329 type=191 (LJ14) 121 132 -62: 330 type=191 (LJ14) 121 133 -62: 331 type=195 (LJ14) 121 135 -62: 332 type=187 (LJ14) 121 136 -62: 333 type=193 (LJ14) 122 125 -62: 334 type=191 (LJ14) 122 126 -62: 335 type=191 (LJ14) 122 130 -62: 336 type=196 (LJ14) 122 134 -62: 337 type=193 (LJ14) 123 125 -62: 338 type=191 (LJ14) 123 126 -62: 339 type=191 (LJ14) 123 130 -62: 340 type=196 (LJ14) 123 134 -62: 341 type=197 (LJ14) 124 134 -62: 342 type=193 (LJ14) 125 127 -62: 343 type=193 (LJ14) 125 128 -62: 344 type=193 (LJ14) 125 129 -62: 345 type=193 (LJ14) 125 131 -62: 346 type=193 (LJ14) 125 132 -62: 347 type=193 (LJ14) 125 133 -62: 348 type=191 (LJ14) 126 131 -62: 349 type=191 (LJ14) 126 132 -62: 350 type=191 (LJ14) 126 133 -62: 351 type=191 (LJ14) 127 130 -62: 352 type=191 (LJ14) 128 130 -62: 353 type=191 (LJ14) 129 130 -62: 354 type=196 (LJ14) 134 139 -62: 355 type=197 (LJ14) 134 140 -62: 356 type=198 (LJ14) 134 144 -62: 357 type=190 (LJ14) 135 137 -62: 358 type=195 (LJ14) 135 138 -62: 359 type=186 (LJ14) 136 141 -62: 360 type=186 (LJ14) 136 142 -62: 361 type=186 (LJ14) 136 143 -62: 362 type=188 (LJ14) 136 145 -62: 363 type=189 (LJ14) 136 146 -62: 364 type=190 (LJ14) 137 139 -62: 365 type=190 (LJ14) 137 140 -62: 366 type=190 (LJ14) 137 144 -62: 367 type=190 (LJ14) 138 147 -62: 368 type=192 (LJ14) 138 148 -62: 369 type=193 (LJ14) 139 141 -62: 370 type=193 (LJ14) 139 142 -62: 371 type=193 (LJ14) 139 143 -62: 372 type=194 (LJ14) 139 145 -62: 373 type=186 (LJ14) 139 146 -62: 374 type=195 (LJ14) 140 145 -62: 375 type=187 (LJ14) 140 146 -62: 376 type=196 (LJ14) 141 144 -62: 377 type=196 (LJ14) 142 144 -62: 378 type=196 (LJ14) 143 144 -62: 379 type=196 (LJ14) 144 149 -62: 380 type=197 (LJ14) 144 150 -62: 381 type=198 (LJ14) 144 154 -62: 382 type=190 (LJ14) 145 147 -62: 383 type=195 (LJ14) 145 148 -62: 384 type=186 (LJ14) 146 151 -62: 385 type=186 (LJ14) 146 152 -62: 386 type=186 (LJ14) 146 153 -62: 387 type=188 (LJ14) 146 155 -62: 388 type=190 (LJ14) 147 149 -62: 389 type=190 (LJ14) 147 150 -62: 390 type=190 (LJ14) 147 154 -62: 391 type=193 (LJ14) 149 151 -62: 392 type=193 (LJ14) 149 152 -62: 393 type=193 (LJ14) 149 153 -62: 394 type=194 (LJ14) 149 155 -62: 395 type=195 (LJ14) 150 155 -62: 396 type=196 (LJ14) 151 154 -62: 397 type=196 (LJ14) 152 154 -62: 398 type=196 (LJ14) 153 154 -62: Coulomb-14: -62: nr: 0 -62: LJC-14 q: -62: nr: 0 -62: LJC Pairs NB: -62: nr: 0 -62: LJ (SR): -62: nr: 0 -62: Buck.ham (SR): -62: nr: 0 -62: LJ: -62: nr: 0 -62: B.ham: -62: nr: 0 -62: Disper. corr.: -62: nr: 0 -62: Coulomb (SR): -62: nr: 0 -62: Coul: -62: nr: 0 -62: RF excl.: -62: nr: 0 -62: Coul. recip.: -62: nr: 0 -62: LJ recip.: -62: nr: 0 -62: DPD: -62: nr: 0 -62: Polarization: -62: nr: 0 -62: Water Pol.: -62: nr: 0 -62: Thole Pol.: -62: nr: 0 -62: Anharm. Pol.: -62: nr: 0 -62: Position Rest.: -62: nr: 0 -62: Flat-b. P-R.: -62: nr: 0 -62: Dis. Rest.: -62: nr: 0 -62: D.R.Viol. (nm): -62: nr: 0 -62: Orient. Rest.: -62: nr: 0 -62: Ori. R. RMSD: -62: nr: 0 -62: Angle Rest.: -62: nr: 0 -62: Angle Rest. Z: -62: nr: 0 -62: Dih. Rest.: -62: nr: 0 -62: Dih. Rest. Vi.: -62: nr: 0 -62: Constraint: -62: nr: 0 -62: Constr. No Co.: -62: nr: 0 -62: Settle: -62: nr: 0 -62: Virtual site 1: -62: nr: 0 -62: Virtual site 2: -62: nr: 0 -62: Virt. site 2fd: -62: nr: 0 -62: Virtual site 3: -62: nr: 0 -62: Virt. site 3fd: -62: nr: 0 -62: Vir. site 3fad: -62: nr: 0 -62: Vir. site 3out: -62: nr: 0 -62: Virt. site 4fd: -62: nr: 0 -62: Vir. site 4fdn: -62: nr: 0 -62: Virtual site N: -62: nr: 0 -62: COM Pull En.: -62: nr: 0 -62: Dens. fitting: -62: nr: 0 -62: Quantum En.: -62: nr: 0 -62: NN Potential: -62: nr: 0 -62: Potential: -62: nr: 0 -62: Kinetic En.: -62: nr: 0 -62: Total Energy: -62: nr: 0 -62: Conserved En.: -62: nr: 0 -62: Temperature: -62: nr: 0 -62: Vir. Temp.: -62: nr: 0 -62: Pres. DC: -62: nr: 0 -62: Pressure: -62: nr: 0 -62: dH/dl constr.: -62: nr: 0 -62: dVremain/dl: -62: nr: 0 -62: dEkin/dl: -62: nr: 0 -62: dVcoul/dl: -62: nr: 0 -62: dVvdw/dl: -62: nr: 0 -62: dVbonded/dl: -62: nr: 0 -62: dVrestraint/dl: -62: nr: 0 -62: dVtemp/dl: -62: nr: 0 -62: grp[T-Coupling ] nr=1, name=[ rest] -62: grp[Energy Mon. ] nr=1, name=[ rest] -62: grp[Acc. not used] nr=1, name=[ rest] -62: grp[Freeze ] nr=1, name=[ rest] -62: grp[User1 ] nr=1, name=[ rest] -62: grp[User2 ] nr=1, name=[ rest] -62: grp[VCM ] nr=1, name=[ rest] -62: grp[Compressed X] nr=1, name=[ rest] -62: grp[Or. Res. Fit] nr=1, name=[ rest] -62: grp[QMMM ] nr=1, name=[ rest] -62: grpname (11): -62: grpname[0]={name="System"} -62: grpname[1]={name="Protein"} -62: grpname[2]={name="Protein-H"} -62: grpname[3]={name="C-alpha"} -62: grpname[4]={name="Backbone"} -62: grpname[5]={name="MainChain"} -62: grpname[6]={name="MainChain+Cb"} -62: grpname[7]={name="MainChain+H"} -62: grpname[8]={name="SideChain"} -62: grpname[9]={name="SideChain-H"} -62: grpname[10]={name="rest"} -62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM -62: allocated 0 0 0 0 0 0 0 0 0 0 -62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 -62: box (3x3): -62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} -62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} -62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} -62: box_rel (3x3): -62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv (3x3): -62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev (3x3): -62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev (3x3): -62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev (3x3): -62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: nosehoover_xi: not available -62: x (156x3): -62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} -62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} -62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} -62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} -62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} -62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} -62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} -62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} -62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} -62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} -62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} -62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} -62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} -62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} -62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} -62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} -62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} -62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} -62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} -62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} -62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} -62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} -62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} -62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} -62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} -62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} -62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} -62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} -62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} -62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} -62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} -62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} -62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} -62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} -62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} -62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} -62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} -62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} -62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} -62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} -62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} -62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} -62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} -62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} -62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} -62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} -62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} -62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} -62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} -62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} -62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} -62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} -62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} -62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} -62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} -62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} -62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} -62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} -62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} -62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} -62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} -62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} -62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} -62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} -62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} -62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} -62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} -62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} -62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} -62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} -62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} -62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} -62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} -62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} -62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} -62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} -62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} -62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} -62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} -62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} -62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} -62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} -62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} -62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} -62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} -62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} -62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} -62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} -62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} -62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} -62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} -62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} -62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} -62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} -62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} -62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} -62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} -62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} -62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} -62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} -62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} -62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} -62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} -62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} -62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} -62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} -62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} -62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} -62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} -62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} -62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} -62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} -62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} -62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} -62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} -62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} -62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} -62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} -62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} -62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} -62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} -62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} -62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} -62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} -62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} -62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} -62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} -62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} -62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} -62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} -62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} -62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} -62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} -62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} -62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} -62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} -62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} -62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} -62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} -62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} -62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} -62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} -62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} -62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} -62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} -62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} -62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} -62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} -62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} -62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} -62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} -62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} -62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} -62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} -62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} -62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} -62: v (156x3): -62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: Group statistics -62: T-Coupling : 156 (total 156 atoms) -62: Energy Mon. : 156 (total 156 atoms) -62: Acc. not used: 156 (total 156 atoms) -62: Freeze : 156 (total 156 atoms) -62: User1 : 156 (total 156 atoms) -62: User2 : 156 (total 156 atoms) -62: VCM : 156 (total 156 atoms) -62: Compressed X: 156 (total 156 atoms) -62: Or. Res. Fit: 156 (total 156 atoms) -62: QMMM : 156 (total 156 atoms) -62: [ OK ] DumpTest.WorksWithTpr (4 ms) -62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) -62: [----------] 2 tests from DumpTest (5 ms total) -62: -62: [----------] 3 tests from HelpwritingTest -62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp -62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) -62: [ RUN ] HelpwritingTest.DumpWritesHelp -62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) -62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp -62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) -62: [----------] 3 tests from HelpwritingTest (0 ms total) -62: -62: [----------] 7 tests from GmxMakeNdx -62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 16 Protein residues -62: Analysing Protein... -62: -62: 0 System : 256 atoms -62: 1 Protein : 256 atoms -62: 2 Protein-H : 139 atoms -62: 3 C-alpha : 16 atoms -62: 4 Backbone : 48 atoms -62: 5 MainChain : 63 atoms -62: 6 MainChain+Cb : 78 atoms -62: 7 MainChain+H : 81 atoms -62: 8 SideChain : 175 atoms -62: 9 SideChain-H : 76 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) -62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput -62: Going to read 1 old index file(s) -62: Deducing 22 atoms in the system from indices in the index file -62: -62: 0 System : 22 atoms -62: 1 Protein : 22 atoms -62: 2 Protein-H : 10 atoms -62: 3 C-alpha : 1 atoms -62: 4 Backbone : 5 atoms -62: 5 MainChain : 7 atoms -62: 6 MainChain+Cb : 8 atoms -62: 7 MainChain+H : 9 atoms -62: 8 SideChain : 13 atoms -62: 9 SideChain-H : 3 atoms -62: 10 CA : 1 atoms -62: 11 C_&_r_1 : 1 atoms -62: 12 C_&_r_2 : 1 atoms -62: 13 N_&_r_2 : 1 atoms -62: 14 N_&_r_3 : 1 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Copied index group 1 'Protein' -62: Copied index group 2 'Protein-H' -62: Merged two groups with OR: 22 10 -> 22 -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (1 ms) -62: [ RUN ] GmxMakeNdx.HandlesNotProtein -62: Going to read 1 old index file(s) -62: Deducing 6 atoms in the system from indices in the index file -62: -62: 0 System : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesNotProtein (1 ms) -62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult -62: Going to read 1 old index file(s) -62: Deducing 22 atoms in the system from indices in the index file -62: -62: 0 System : 22 atoms -62: 1 Protein : 22 atoms -62: 2 Protein-H : 10 atoms -62: 3 C-alpha : 1 atoms -62: 4 Backbone : 5 atoms -62: 5 MainChain : 7 atoms -62: 6 MainChain+Cb : 8 atoms -62: 7 MainChain+H : 9 atoms -62: 8 SideChain : 13 atoms -62: 9 SideChain-H : 3 atoms -62: 10 CA : 1 atoms -62: 11 C_&_r_1 : 1 atoms -62: 12 C_&_r_2 : 1 atoms -62: 13 N_&_r_2 : 1 atoms -62: 14 N_&_r_3 : 1 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Copied index group 4 'Backbone' -62: Copied index group 8 'SideChain' -62: Merged two groups with AND: 5 13 -> 0 -62: Group is empty -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (1 ms) -62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile -62: Going to read 1 old index file(s) -62: Deducing 6 atoms in the system from indices in the index file -62: -62: 0 System : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Removed group 0 'System' -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) -62: [ RUN ] GmxMakeNdx.Splitres -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 2 Water residues -62: -62: 0 System : 6 atoms -62: 1 Water : 6 atoms -62: 2 SOL : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Splitting group 1 'Water' into residues -62: -62: > -62: [ OK ] GmxMakeNdx.Splitres (0 ms) -62: [ RUN ] GmxMakeNdx.Splitat -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 2 Water residues -62: -62: 0 System : 6 atoms -62: 1 Water : 6 atoms -62: 2 SOL : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Splitting group 1 'Water' into atoms -62: -62: > -62: [ OK ] GmxMakeNdx.Splitat (0 ms) -62: [----------] 7 tests from GmxMakeNdx (9 ms total) -62: -62: [----------] 4 tests from ReportMethodsTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Setting the LD random seed to -1082139150 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated -62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) -62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted -62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) -62: [ RUN ] ReportMethodsTest.WritesCorrectInformation -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) -62: [ RUN ] ReportMethodsTest.ToolEndToEndTest -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: section: Methods -62: subsection: Simulation system -62: A system of 1 molecules (156 atoms) was simulated. -62: -62: subsection: Simulation settings -62: A total of 0 ns were simulated with a time step of 1 fs. -62: Neighbor searching was performed every 10 steps. -62: The Cut-off algorithm was used for electrostatic interactions. -62: with a cut-off of 1 nm. -62: A single cut-off of 1.1 nm was used for Van der Waals interactions. -62: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) -62: [----------] 4 tests from ReportMethodsTest (1 ms total) -62: -62: [----------] 4 tests from ConvertTprTest -62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -1091045457 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: Extending remaining runtime by 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: Extending remaining runtime by 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 200000 -62: Runtime for the run 200 ps -62: Run end step 200000 -62: Run end time 200 ps -62: -62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (273 ms) -62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -168865815 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: Extending remaining runtime to 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (376 ms) -62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting nsteps to 102 -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -1225785633 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 102 -62: Runtime for the run 0.102 ps -62: Run end step 102 -62: Run end time 0.102 ps -62: -62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (324 ms) -62: [ RUN ] ConvertTprTest.generateVelocitiesTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -49283 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] ConvertTprTest.generateVelocitiesTest (436 ms) -62: [----------] 4 tests from ConvertTprTest (1411 ms total) -62: -62: [----------] 1 test from ConvertTprNoVelocityTest -62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: -62: NOTE 3 [file lysozyme.top, line 1465]: -62: Zero-step energy minimization will alter the coordinates before -62: calculating the energy. If you just want the energy of a single point, -62: try zero-step MD (with unconstrained_start = yes). To do multiple -62: single-point energy evaluations of different configurations of the same -62: topology, use mdrun -rerun. -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -329779201 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (378 ms) -62: [----------] 1 test from ConvertTprNoVelocityTest (378 ms total) -62: -62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: trr version: GMX_trn_file (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) -62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (9 ms total) -62: -62: [----------] 30 tests from Works/TrjconvDumpTest -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) -62: [----------] 30 tests from Works/TrjconvDumpTest (15 ms total) -62: -62: [----------] Global test environment tear-down -62: [==========] 63 tests from 8 test suites ran. (2273 ms total) -62: [ PASSED ] 63 tests. -62/92 Test #62: ToolUnitTests ............................. Passed 2.29 sec -test 63 - Start 63: ToolWithLeaksUnitTests - -63: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" -63: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests -63: Test timeout computed to be: 1920 -63: [==========] Running 2 tests from 2 test suites. -63: [----------] Global test environment set-up. -63: [----------] 1 test from ConvertTprTest -63: [ RUN ] ConvertTprTest.selectIndexTest -63: -63: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: For a correct single-point energy evaluation with nsteps = 0, use -63: continuation = yes to avoid constraining the input coordinates. -63: -63: Generating 1-4 interactions: fudge = 0.5 -63: -63: NOTE 2 [file lysozyme.top, line 1465]: -63: System has non-zero total charge: 2.000000 -63: Total charge should normally be an integer. See -63: https://manual.gromacs.org/current/user-guide/floating-point.html -63: for discussion on how close it should be to an integer. -63: -63: -63: -63: Number of degrees of freedom in T-Coupling group rest is 465.00 -63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -63: -63: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: NVE simulation with an initial temperature of zero: will use a Verlet -63: buffer of 10%. Check your energy drift! -63: -63: -63: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: You are using a plain Coulomb cut-off, which might produce artifacts. -63: You might want to consider using PME electrostatics. -63: -63: -63: -63: There were 4 NOTEs -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Group 0 ( System) has 156 elements -63: Group 1 ( Protein) has 156 elements -63: Group 2 ( Protein-H) has 75 elements -63: Group 3 ( C-alpha) has 10 elements -63: Group 4 ( Backbone) has 30 elements -63: Group 5 ( MainChain) has 40 elements -63: Group 6 ( MainChain+Cb) has 49 elements -63: Group 7 ( MainChain+H) has 52 elements -63: Group 8 ( SideChain) has 104 elements -63: Group 9 ( SideChain-H) has 35 elements -63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -63: Reduced ilist BONDS from 156 to 75 entries -63: Reduced ilist ANGLES from 281 to 98 entries -63: Reduced ilist PDIHS from 29 to 12 entries -63: Reduced ilist RBDIHS from 313 to 89 entries -63: Reduced ilist LJ14 from 399 to 107 entries -63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Setting the LD random seed to -42270760 -63: -63: Generated 330891 of the 330891 non-bonded parameter combinations -63: -63: Generated 330891 of the 330891 1-4 parameter combinations -63: -63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -63: -63: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -63: Analysing residue names: -63: There are: 10 Protein residues -63: Analysing Protein... -63: -63: This run will generate roughly 0 Mb of data -63: Selected 2: 'Protein-H' -63: [ OK ] ConvertTprTest.selectIndexTest (295 ms) -63: [----------] 1 test from ConvertTprTest (295 ms total) -63: -63: [----------] 1 test from ConvertTprNoVelocityTest -63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity -63: -63: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -63: For a correct single-point energy evaluation with nsteps = 0, use -63: continuation = yes to avoid constraining the input coordinates. -63: -63: Generating 1-4 interactions: fudge = 0.5 -63: -63: NOTE 2 [file lysozyme.top, line 1465]: -63: System has non-zero total charge: 2.000000 -63: Total charge should normally be an integer. See -63: https://manual.gromacs.org/current/user-guide/floating-point.html -63: for discussion on how close it should be to an integer. -63: -63: -63: -63: -63: NOTE 3 [file lysozyme.top, line 1465]: -63: Zero-step energy minimization will alter the coordinates before -63: calculating the energy. If you just want the energy of a single point, -63: try zero-step MD (with unconstrained_start = yes). To do multiple -63: single-point energy evaluations of different configurations of the same -63: topology, use mdrun -rerun. -63: -63: Number of degrees of freedom in T-Coupling group rest is 465.00 -63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -63: -63: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -63: You are using a plain Coulomb cut-off, which might produce artifacts. -63: You might want to consider using PME electrostatics. -63: -63: -63: -63: There were 4 NOTEs -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Group 0 ( System) has 156 elements -63: Group 1 ( Protein) has 156 elements -63: Group 2 ( Protein-H) has 75 elements -63: Group 3 ( C-alpha) has 10 elements -63: Group 4 ( Backbone) has 30 elements -63: Group 5 ( MainChain) has 40 elements -63: Group 6 ( MainChain+Cb) has 49 elements -63: Group 7 ( MainChain+H) has 52 elements -63: Group 8 ( SideChain) has 104 elements -63: Group 9 ( SideChain-H) has 35 elements -63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -63: Reduced ilist BONDS from 156 to 75 entries -63: Reduced ilist ANGLES from 281 to 98 entries -63: Reduced ilist PDIHS from 29 to 12 entries -63: Reduced ilist RBDIHS from 313 to 89 entries -63: Reduced ilist LJ14 from 399 to 107 entries -63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -63: Setting the LD random seed to -237252641 -63: -63: Generated 330891 of the 330891 non-bonded parameter combinations -63: -63: Generated 330891 of the 330891 1-4 parameter combinations -63: -63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -63: Analysing residue names: -63: There are: 10 Protein residues -63: Analysing Protein... -63: -63: This run will generate roughly 0 Mb of data -63: Selected 2: 'Protein-H' -63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (333 ms) -63: [----------] 1 test from ConvertTprNoVelocityTest (333 ms total) -63: -63: [----------] Global test environment tear-down -63: [==========] 2 tests from 2 test suites ran. (629 ms total) -63: [ PASSED ] 2 tests. -63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 0.64 sec -test 64 - Start 64: FileIOTests - -64: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/FileIOTests.xml" -64: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/fileio/tests -64: Test timeout computed to be: 30 -64: [==========] Running 421 tests from 17 test suites. -64: [----------] Global test environment set-up. -64: [----------] 4 tests from Checkpoint -64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent -64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) -64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent -64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) -64: [ RUN ] Checkpoint.KvtRoundTripInt64 -64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) -64: [ RUN ] Checkpoint.KvtRoundTripReal -64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) -64: [----------] 4 tests from Checkpoint (0 ms total) -64: -64: [----------] 1 test from StructureIOTest -64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids -64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) -64: [----------] 1 test from StructureIOTest (0 ms total) -64: -64: [----------] 2 tests from FileMD5Test -64: [ RUN ] FileMD5Test.CanComputeMD5 -64: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) -64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong -64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) -64: [----------] 2 tests from FileMD5Test (1 ms total) -64: -64: [----------] 4 tests from FileTypeTest -64: [ RUN ] FileTypeTest.CorrectValueForEmptyString -64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForNoExtension -64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension -64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters -64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) -64: [----------] 4 tests from FileTypeTest (0 ms total) -64: -64: [----------] 4 tests from ColorMapTest -64: [ RUN ] ColorMapTest.CanReadFromFile -64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) -64: [ RUN ] ColorMapTest.CanWriteToFile -64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) -64: [ RUN ] ColorMapTest.RoundTrip -64: [ OK ] ColorMapTest.RoundTrip (0 ms) -64: [ RUN ] ColorMapTest.SearchWorks -64: [ OK ] ColorMapTest.SearchWorks (0 ms) -64: [----------] 4 tests from ColorMapTest (1 ms total) -64: -64: [----------] 4 tests from MatioTest -64: [ RUN ] MatioTest.CanWriteToFile -64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) -64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix -64: Converted a 4x3 matrix with 4 levels to reals -64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) -64: [ RUN ] MatioTest.CanConvertToNewRealMatrix -64: Converted a 4x3 matrix with 4 levels to reals -64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) -64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting -64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (2 ms) -64: [----------] 4 tests from MatioTest (3 ms total) -64: -64: [----------] 3 tests from MrcSerializer -64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet -64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) -64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize -64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) -64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip -64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) -64: [----------] 3 tests from MrcSerializer (0 ms total) -64: -64: [----------] 4 tests from MrcDensityMap -64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent -64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) -64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent -64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) -64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile -64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) -64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile -64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) -64: [----------] 4 tests from MrcDensityMap (1 ms total) -64: -64: [----------] 8 tests from MrcDensityMapHeaderTest -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader -64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect -64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid -64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.IsSane -64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) -64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) -64: -64: [----------] 10 tests from ReadTest -64: [ RUN ] ReadTest.get_eint_ReadsInteger -64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat -64: -64: ERROR 1 [file unknown]: -64: Right hand side '0.8' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) -64: [ RUN ] ReadTest.get_eint_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.get_eint64_ReadsInteger -64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat -64: -64: ERROR 1 [file unknown]: -64: Right hand side '0.8' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) -64: [ RUN ] ReadTest.get_eint64_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.get_ereal_ReadsInteger -64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_ereal_ReadsFloat -64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) -64: [ RUN ] ReadTest.get_ereal_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not a -64: real value -64: -64: -64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString -64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) -64: [----------] 10 tests from ReadTest (0 ms total) -64: -64: [----------] 3 tests from TimeControlTest -64: [ RUN ] TimeControlTest.UnSetHasNoValue -64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) -64: [ RUN ] TimeControlTest.CanSetValue -64: [ OK ] TimeControlTest.CanSetValue (0 ms) -64: [ RUN ] TimeControlTest.CanUnsetValueAgain -64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) -64: [----------] 3 tests from TimeControlTest (0 ms total) -64: -64: [----------] 1 test from FileIOXdrSerializerTest -64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect -64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) -64: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) -64: -64: [----------] 1 test from TngTest -64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal -64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) -64: [----------] 1 test from TngTest (0 ms total) -64: -64: [----------] 4 tests from XvgioTest -64: [ RUN ] XvgioTest.readXvgIntWorks -64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgRealWorks -64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks -64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgDeprecatedWorks -64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) -64: [----------] 4 tests from XvgioTest (0 ms total) -64: -64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) -64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (1 ms total) -64: -64: [----------] 360 tests from FileTypeMatch/FileTypeTest -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) -64: [----------] 360 tests from FileTypeMatch/FileTypeTest (2 ms total) -64: -64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (2 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) -64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (3 ms total) -64: -64: [----------] Global test environment tear-down -64: [==========] 421 tests from 17 test suites ran. (18 ms total) -64: [ PASSED ] 421 tests. -64/92 Test #64: FileIOTests ............................... Passed 0.04 sec -test 65 - Start 65: SelectionUnitTests - -65: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/SelectionUnitTests.xml" -65: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/tests -65: Test timeout computed to be: 30 -65: [==========] Running 201 tests from 11 test suites. -65: [----------] Global test environment set-up. -65: [----------] 1 test from IndexGroupTest -65: [ RUN ] IndexGroupTest.RemovesDuplicates -65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) -65: [----------] 1 test from IndexGroupTest (0 ms total) -65: -65: [----------] 15 tests from IndexBlockTest -65: [ RUN ] IndexBlockTest.CreatesUnknownBlock -65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) -65: [ RUN ] IndexBlockTest.CreatesAtomBlock -65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) -65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology -65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology -65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology -65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology -65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesSingleBlock -65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive -65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive -65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative -65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) -65: [----------] 15 tests from IndexBlockTest (1 ms total) -65: -65: [----------] 11 tests from IndexMapTest -65: [ RUN ] IndexMapTest.InitializesAtomBlock -65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom -65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle -65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue -65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule -65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll -65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) -65: [ RUN ] IndexMapTest.InitializesMoleculeBlock -65: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) -65: [ RUN ] IndexMapTest.MapsSingleBlock -65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) -65: [ RUN ] IndexMapTest.MapsResidueBlocks -65: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) -65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask -65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) -65: [ RUN ] IndexMapTest.HandlesMultipleRequests -65: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) -65: [----------] 11 tests from IndexMapTest (1 ms total) -65: -65: [----------] 3 tests from IndexGroupsAndNamesTest -65: [ RUN ] IndexGroupsAndNamesTest.containsNames -65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) -65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing -65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) -65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect -65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) -65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) -65: -65: [----------] 15 tests from NeighborhoodSearchTest -65: [ RUN ] NeighborhoodSearchTest.SimpleSearch -65: [ OK ] NeighborhoodSearchTest.SimpleSearch (10 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY -65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (9 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchBox -65: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic -65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (5 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC -65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC -65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox -65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch -65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch -65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (28 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches -65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC -65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC -65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs -65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions -65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions -65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) -65: [----------] 15 tests from NeighborhoodSearchTest (64 ms total) -65: -65: [----------] 13 tests from PositionCalculationTest -65: [ RUN ] PositionCalculationTest.ComputesAtomPositions -65: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex -65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions -65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions -65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions -65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions -65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole -65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax -65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionMask -65: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms -65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 -65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations -65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations -65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) -65: [----------] 13 tests from PositionCalculationTest (3 ms total) -65: -65: [----------] 33 tests from SelectionCollectionTest -65: [ RUN ] SelectionCollectionTest.HandlesNoSelections -65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType -65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests -65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry -65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) -65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile -65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace -65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions -65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference -65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed -65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo -65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes -65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo -65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) -65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection -65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) -65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection -65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) -65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection -65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) -65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately -65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) -65: [----------] 33 tests from SelectionCollectionTest (10 ms total) -65: -65: [----------] 14 tests from SelectionCollectionInteractiveTest -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation -65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups -65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections -65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline -65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections -65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine -65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) -65: [----------] 14 tests from SelectionCollectionInteractiveTest (4 ms total) -65: -65: [----------] 70 tests from SelectionCollectionDataTest -65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone -65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr -65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResnr -65: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex -65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex -65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname -65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname -65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype -65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesChain -65: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMass -65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesCharge -65: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc -65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode -65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy -65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBeta -65: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResname -65: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue -65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName -65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier -65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) -65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges -65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) -65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology -65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets -65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames -65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections -65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed -65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections -65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed -65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions -65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges -65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges -65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode -65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching -65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching -65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean -65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters -65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions -65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame -65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods -65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions -65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic -65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons -65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions -65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables -65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables -65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables -65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables -65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables -65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) -65: [----------] 70 tests from SelectionCollectionDataTest (54 ms total) -65: -65: [----------] 17 tests from SelectionOptionTest -65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection -65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired -65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired -65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired -65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksEmptySelections -65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections -65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooManySelections -65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections -65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText -65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesAdjuster -65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection -65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections -65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection -65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) -65: [----------] 17 tests from SelectionOptionTest (4 ms total) -65: -65: [----------] 9 tests from SelectionFileOptionTest -65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile -65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions -65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile -65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile -65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet -65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile -65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile -65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile -65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles -65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) -65: [----------] 9 tests from SelectionFileOptionTest (2 ms total) -65: -65: [----------] Global test environment tear-down -65: [==========] 201 tests from 11 test suites ran. (147 ms total) -65: [ PASSED ] 201 tests. -65/92 Test #65: SelectionUnitTests ........................ Passed 0.16 sec -test 66 - Start 66: MdrunOutputTests - -66: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunOutputTests.xml" -66: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -66: Test timeout computed to be: 600 -66: [==========] Running 12 tests from 5 test suites. -66: [----------] Global test environment set-up. -66: [----------] 1 test from MdrunTest -66: [ RUN ] MdrunTest.WritesHelp -66: [ OK ] MdrunTest.WritesHelp (72 ms) -66: [----------] 1 test from MdrunTest (72 ms total) -66: -66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -479478185 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.075 0.038 199.6 -66: (ns/day) (hour/ns) -66: Performance: 4.603 5.214 -66: Reading frame 0 time 0.000 -66: # Atoms 6 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (87 ms) -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -820668 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.047 0.024 199.4 -66: (ns/day) (hour/ns) -66: Performance: 7.337 3.271 -66: Reading frame 0 time 0.000 -66: # Atoms 6 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (33 ms) -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -1208229891 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.051 0.026 199.4 -66: (ns/day) (hour/ns) -66: Performance: 6.711 3.576 -66: Reading frame 0 time 0.000 -66: # Atoms 3 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (32 ms) -66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (153 ms total) -66: -66: [----------] 2 tests from Argon12/OutputFiles -66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -66: that with the Verlet scheme, nstlist has no effect on the accuracy of -66: your simulation. -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: Setting nstcalcenergy (100) equal to nstenergy (4) -66: -66: Number of degrees of freedom in T-Coupling group System is 33.00 -66: -66: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: NVE simulation: will use the initial temperature of 68.810 K for -66: determining the Verlet buffer size -66: -66: -66: There were 3 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'Argon' -66: 16 steps, 0.0 ps. -66: Generated 1 of the 1 non-bonded parameter combinations -66: -66: Excluding 1 bonded neighbours molecule type 'Argon' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -66: -66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -66: -66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.034 0.017 199.4 -66: (ns/day) (hour/ns) -66: Performance: 86.315 0.278 -66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (23 ms) -66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -66: that with the Verlet scheme, nstlist has no effect on the accuracy of -66: your simulation. -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: Setting nstcalcenergy (100) equal to nstenergy (4) -66: -66: Number of degrees of freedom in T-Coupling group System is 33.00 -66: -66: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: NVE simulation: will use the initial temperature of 68.810 K for -66: determining the Verlet buffer size -66: -66: -66: There were 3 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'Argon' -66: 16 steps, 0.0 ps. -66: Generated 1 of the 1 non-bonded parameter combinations -66: -66: Excluding 1 bonded neighbours molecule type 'Argon' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -66: -66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -66: -66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.018 0.009 199.0 -66: (ns/day) (hour/ns) -66: Performance: 163.785 0.147 -66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (15 ms) -66: [----------] 2 tests from Argon12/OutputFiles (39 ms total) -66: -66: [----------] 3 tests from MdrunCanWrite/Trajectories -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to -289410401 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.092 0.046 199.8 -66: (ns/day) (hour/ns) -66: Performance: 13.096 1.833 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (58 ms) -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to 2147434430 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.087 0.044 199.6 -66: (ns/day) (hour/ns) -66: Performance: 13.897 1.727 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (57 ms) -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to -1380450824 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.101 0.051 199.8 -66: (ns/day) (hour/ns) -66: Performance: 11.927 2.012 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (56 ms) -66: [----------] 3 tests from MdrunCanWrite/Trajectories (172 ms total) -66: -66: [----------] 3 tests from MdrunCanWrite/NptTrajectories -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to 978908543 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.015 0.008 198.5 -66: (ns/day) (hour/ns) -66: Performance: 34.134 0.703 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (13 ms) -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 -66: -66: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -66: The Berendsen barostat does not generate any strictly correct ensemble, -66: and should not be used for new production simulations (in our opinion). -66: We recommend using the C-rescale barostat instead. -66: -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: -66: There was 1 WARNING -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to -1642164247 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.224 0.112 199.9 -66: (ns/day) (hour/ns) -66: Performance: 2.309 10.392 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (117 ms) -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to -513903109 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.317 0.159 199.9 -66: (ns/day) (hour/ns) -66: Performance: 1.635 14.681 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (168 ms) -66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (300 ms total) -66: -66: [----------] Global test environment tear-down -66: [==========] 12 tests from 5 test suites ran. (940 ms total) -66: [ PASSED ] 12 tests. -66/92 Test #66: MdrunOutputTests .......................... Passed 0.95 sec -test 67 - Start 67: MdrunModulesTests - -67: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunModulesTests.xml" -67: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -67: Test timeout computed to be: 600 -67: [==========] Running 15 tests from 3 test suites. -67: [----------] Global test environment set-up. -67: [----------] 9 tests from DensityFittingTest -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -3.8565254e+03 -67: Maximum force = 4.5099883e+03 on atom 3 -67: Norm of force = 1.6816849e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -134833153 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (10 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -9.8207725e+03 -67: Maximum force = 7.3954834e+03 on atom 2 -67: Norm of force = 2.7825089e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -403577099 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (6 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (6 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Overriding nsteps with value passed on the command line: 4 steps -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 4 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 5 steps. -67: Potential Energy = -5.4739302e+03 -67: Maximum force = 6.1322041e+03 on atom 2 -67: Norm of force = 1.7702155e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -35672580 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (6 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (6 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -3.8565254e+03 -67: Maximum force = 4.5099883e+03 on atom 3 -67: Norm of force = 1.6816849e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -874849433 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (7 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -2.7138664e+04 -67: Maximum force = 6.7827656e+03 on atom 2 -67: Norm of force = 1.9608866e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1073512175 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (10 ms) -67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: Setting the LD random seed to -202506337 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (5 ms) -67: [ RUN ] DensityFittingTest.CheckpointWorks -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -67: Setting nstcalcenergy (100) equal to nstenergy (2) -67: -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -67: NVE simulation: will use the initial temperature of 68.810 K for -67: determining the Verlet buffer size -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting mdrun 'Argon' -67: 2 steps, 0.0 ps. -67: Setting the LD random seed to -536937229 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.027 0.013 199.2 -67: (ns/day) (hour/ns) -67: Performance: 19.206 1.250 -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps -67: Can not increase nstlist because an NVE ensemble is used -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting mdrun 'Argon' -67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.040 0.020 199.1 -67: (ns/day) (hour/ns) -67: Performance: 21.256 1.129 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (42 ms) -67: [----------] 9 tests from DensityFittingTest (101 ms total) -67: -67: [----------] 4 tests from MimicTest -67: [ RUN ] MimicTest.OneQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 27 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.000 0.000 185.6 -67: (ns/day) (hour/ns) -67: Performance: 371.680 0.065 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -10930 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.OneQuantumMol (4 ms) -67: [ RUN ] MimicTest.AllQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 21 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.000 0.000 186.1 -67: (ns/day) (hour/ns) -67: Performance: 420.404 0.057 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1985953463 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.AllQuantumMol (4 ms) -67: [ RUN ] MimicTest.TwoQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 28 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.000 0.000 186.8 -67: (ns/day) (hour/ns) -67: Performance: 411.337 0.058 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -727180 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.TwoQuantumMol (7 ms) -67: [ RUN ] MimicTest.BondCuts -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 66.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: NVE simulation: will use the initial temperature of 300.368 K for -67: determining the Verlet buffer size -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -67: -67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 18 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.001 0.000 183.5 -67: (ns/day) (hour/ns) -67: Performance: 173.474 0.138 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1747199057 -67: -67: Generated 2211 of the 2211 non-bonded parameter combinations -67: -67: Generated 2211 of the 2211 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.BondCuts (11 ms) -67: [----------] 4 tests from MimicTest (28 ms total) -67: -67: [----------] 2 tests from WithIntegrator/ImdTest -67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 -67: Generating 1-4 interactions: fudge = 1 -67: -67: NOTE 1 [file glycine_vacuo.top, line 12]: -67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an -67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times -67: the time step of 2.0e-03 ps. -67: Maybe you forgot to change the constraints mdp option. -67: -67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -67: Number of degrees of freedom in T-Coupling group System is 27.00 -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: IMD: Enabled. This simulation will accept incoming IMD connections. -67: IMD: Pulling from IMD remote is enabled (-imdpull). -67: IMD: Setting port for connection requests to 0. -67: IMD: Setting up incoming socket. -67: IMD: Listening for IMD connection on port 43535. -67: IMD: -imdwait not set, starting simulation. -67: starting mdrun 'Glycine' -67: 2 steps, 0.0 ps. -67: Setting the LD random seed to -4915205 -67: -67: Generated 20503 of the 20503 non-bonded parameter combinations -67: -67: Generated 17396 of the 20503 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Glycine' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.051 0.026 199.5 -67: (ns/day) (hour/ns) -67: Performance: 20.270 1.184 -67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (95 ms) -67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not -67: apply to steep. -67: -67: Generating 1-4 interactions: fudge = 1 -67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -67: Number of degrees of freedom in T-Coupling group System is 27.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: IMD: Enabled. This simulation will accept incoming IMD connections. -67: IMD: Pulling from IMD remote is enabled (-imdpull). -67: IMD: Setting port for connection requests to 0. -67: IMD: Setting up incoming socket. -67: IMD: Listening for IMD connection on port 56375. -67: IMD: -imdwait not set, starting simulation. -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = 1.1977064e+03 -67: Maximum force = 1.7794877e+04 on atom 9 -67: Norm of force = 7.8732901e+03 -67: Setting the LD random seed to -508102657 -67: -67: Generated 20503 of the 20503 non-bonded parameter combinations -67: -67: Generated 17396 of the 20503 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Glycine' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (63 ms) -67: [----------] 2 tests from WithIntegrator/ImdTest (158 ms total) -67: -67: [----------] Global test environment tear-down -67: [==========] 15 tests from 3 test suites ran. (441 ms total) -67: [ PASSED ] 15 tests. -67/92 Test #67: MdrunModulesTests ......................... Passed 0.46 sec -test 68 - Start 68: MdrunIOTests - -68: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunIOTests.xml" -68: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -68: Test timeout computed to be: 600 -68: [==========] Running 76 tests from 13 test suites. -68: [----------] Global test environment set-up. -68: [----------] 9 tests from GromppTest -68: [ RUN ] GromppTest.EmptyMdpFileWorks -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -1695933221 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.EmptyMdpFileWorks (5 ms) -68: [ RUN ] GromppTest.SimulatedAnnealingWorks -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Simulated annealing for group rest: Periodic, 4 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 2.0 320.0 -68: 4.0 320.0 -68: 6.0 298.0 -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -1073750042 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.SimulatedAnnealingWorks (6 ms) -68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Simulated annealing for group Methanol: Single, 3 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 3.0 280.0 -68: 6.0- 270.0 -68: Simulated annealing for group SOL: Periodic, 4 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 2.0 320.0 -68: 4.0 320.0 -68: 6.0 298.0 -68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 -68: Number of degrees of freedom in T-Coupling group SOL is 4.80 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to 1876769101 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (3 ms) -68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError -68: Setting the LD random seed to -1417747471 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (6 ms) -68: [ RUN ] GromppTest.HandlesMaxwarn -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: -68: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: The Berendsen thermostat does not generate the correct kinetic energy -68: distribution, and should not be used for new production simulations (in -68: our opinion). We would recommend the V-rescale thermostat. -68: -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: -68: There was 1 WARNING -68: Setting the LD random seed to -16908804 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.HandlesMaxwarn (3 ms) -68: [ RUN ] GromppTest.MaxwarnShouldBePositive -68: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) -68: [ RUN ] GromppTest.ValidTransformationCoord -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Pull group 1 'SOL' has 3 atoms -68: Pull group 2 'Methanol' has 3 atoms -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -1108089100 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.ValidTransformationCoord (7 ms) -68: [ RUN ] GromppTest.InvalidTransformationCoord -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Pull group 1 'SOL' has 3 atoms -68: Pull group 2 'Methanol' has 3 atoms -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: 1 3 5 -68: 2 3 2 Setting the LD random seed to -1617105153 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: [ OK ] GromppTest.InvalidTransformationCoord (4 ms) -68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic -68: Setting the LD random seed to -943928627 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (15 ms) -68: [----------] 9 tests from GromppTest (54 ms total) -68: -68: [----------] 6 tests from MdrunTerminationTest -68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -216039952 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.106 0.053 199.8 -68: (ns/day) (hour/ns) -68: Performance: 4.868 4.930 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.008 0.004 198.1 -68: (ns/day) (hour/ns) -68: Performance: 64.747 0.371 -68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (67 ms) -68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 100 steps, 0.1 ps. -68: -68: Step 4: Run time exceeded 0.000 hours, will terminate the run within 200 steps -68: Setting the LD random seed to -37519682 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: NOTE: 16 % of the run time was spent in pair search, -68: you might want to increase nstlist (this has no effect on accuracy) -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.4 -68: (ns/day) (hour/ns) -68: Performance: 545.196 0.044 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 102 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 100 -68: Runtime for the run 0.1 ps -68: Run end step 100 -68: Run end time 0.1 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 102 -68: Runtime for the run 0.102 ps -68: Run end step 102 -68: Run end time 0.102 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.011 0.006 197.6 -68: (ns/day) (hour/ns) -68: Performance: 46.838 0.512 -68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (31 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -807093004 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.007 198.6 -68: (ns/day) (hour/ns) -68: Performance: 35.108 0.684 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.015 199.3 -68: (ns/day) (hour/ns) -68: Performance: 16.885 1.421 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 6 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 6 -68: Runtime for the run 0.006 ps -68: Run end step 6 -68: Run end time 0.006 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.4 -68: (ns/day) (hour/ns) -68: Performance: 29.235 0.821 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 8 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 6 -68: Runtime for the run 0.006 ps -68: Run end step 6 -68: Run end time 0.006 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 8 -68: Runtime for the run 0.008 ps -68: Run end step 8 -68: Run end time 0.008 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 199.5 -68: (ns/day) (hour/ns) -68: Performance: 33.298 0.721 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: NOTE: 24 % of the run time was spent in pair search, -68: you might want to increase nstlist (this has no effect on accuracy) -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.000 0.000 172.9 -68: (ns/day) (hour/ns) -68: Performance: 654.130 0.037 -68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (62 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -1346375429 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 199.2 -68: (ns/day) (hour/ns) -68: Performance: 36.837 0.652 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps. -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 199.5 -68: (ns/day) (hour/ns) -68: Performance: 37.956 0.632 -68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (27 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -16910353 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.097 0.048 199.8 -68: (ns/day) (hour/ns) -68: Performance: 5.362 4.476 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 4 -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (67 ms) -68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -1493437954 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.056 0.028 199.4 -68: (ns/day) (hour/ns) -68: Performance: 9.234 2.599 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.044 0.022 199.7 -68: (ns/day) (hour/ns) -68: Performance: 11.647 2.061 -68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (62 ms) -68: [----------] 6 tests from MdrunTerminationTest (318 ms total) -68: -68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks -68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 198.5 -68: (ns/day) (hour/ns) -68: Performance: 169.629 0.141 -68: trr version: GMX_trn_file (single precision) -68: -68: -68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (14 ms) -68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.012 199.3 -68: (ns/day) (hour/ns) -68: Performance: 126.014 0.190 -68: -68: -68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (19 ms) -68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (34 ms total) -68: -68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.6 -68: (ns/day) (hour/ns) -68: Performance: 159.721 0.150 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.020 199.5 -68: (ns/day) (hour/ns) -68: Performance: 39.492 0.608 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.012 198.8 -68: (ns/day) (hour/ns) -68: Performance: 62.567 0.384 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (65 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.8 -68: (ns/day) (hour/ns) -68: Performance: 121.816 0.197 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 79.562 0.302 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 68.676 0.349 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (66 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.3 -68: (ns/day) (hour/ns) -68: Performance: 97.581 0.246 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.010 199.3 -68: (ns/day) (hour/ns) -68: Performance: 75.285 0.319 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.0 -68: (ns/day) (hour/ns) -68: Performance: 51.808 0.463 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (60 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.041 0.021 199.5 -68: (ns/day) (hour/ns) -68: Performance: 71.306 0.337 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 199.4 -68: (ns/day) (hour/ns) -68: Performance: 89.557 0.268 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.5 -68: (ns/day) (hour/ns) -68: Performance: 75.396 0.318 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (57 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.012 199.0 -68: (ns/day) (hour/ns) -68: Performance: 117.836 0.204 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.1 -68: (ns/day) (hour/ns) -68: Performance: 84.534 0.284 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.012 199.3 -68: (ns/day) (hour/ns) -68: Performance: 62.380 0.385 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (50 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.6 -68: (ns/day) (hour/ns) -68: Performance: 148.280 0.162 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 71.856 0.334 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.9 -68: (ns/day) (hour/ns) -68: Performance: 65.400 0.367 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (51 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.5 -68: (ns/day) (hour/ns) -68: Performance: 160.190 0.150 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.5 -68: (ns/day) (hour/ns) -68: Performance: 77.621 0.309 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 199.2 -68: (ns/day) (hour/ns) -68: Performance: 46.161 0.520 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (54 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 199.2 -68: (ns/day) (hour/ns) -68: Performance: 85.509 0.281 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.1 -68: (ns/day) (hour/ns) -68: Performance: 60.668 0.396 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.0 -68: (ns/day) (hour/ns) -68: Performance: 78.564 0.305 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (63 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.009 198.8 -68: (ns/day) (hour/ns) -68: Performance: 156.277 0.154 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.8 -68: (ns/day) (hour/ns) -68: Performance: 63.827 0.376 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.2 -68: (ns/day) (hour/ns) -68: Performance: 83.577 0.287 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (49 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.038 0.019 199.4 -68: (ns/day) (hour/ns) -68: Performance: 77.426 0.310 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 76.624 0.313 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.033 0.016 199.3 -68: (ns/day) (hour/ns) -68: Performance: 47.197 0.509 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (64 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.222 0.111 199.9 -68: (ns/day) (hour/ns) -68: Performance: 13.257 1.810 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.286 0.143 199.9 -68: (ns/day) (hour/ns) -68: Performance: 5.439 4.412 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.0 -68: (ns/day) (hour/ns) -68: Performance: 71.072 0.338 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (279 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 138.655 0.173 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 72.206 0.332 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 198.6 -68: (ns/day) (hour/ns) -68: Performance: 72.259 0.332 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (50 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.6 -68: (ns/day) (hour/ns) -68: Performance: 151.802 0.158 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 81.003 0.296 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.2 -68: (ns/day) (hour/ns) -68: Performance: 87.124 0.275 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (46 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.2 -68: (ns/day) (hour/ns) -68: Performance: 150.891 0.159 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 199.2 -68: (ns/day) (hour/ns) -68: Performance: 61.650 0.389 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.0 -68: (ns/day) (hour/ns) -68: Performance: 73.985 0.324 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (52 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.1 -68: (ns/day) (hour/ns) -68: Performance: 166.606 0.144 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 199.3 -68: (ns/day) (hour/ns) -68: Performance: 45.309 0.530 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.012 198.8 -68: (ns/day) (hour/ns) -68: Performance: 66.508 0.361 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (55 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 151.545 0.158 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.347 0.174 199.9 -68: (ns/day) (hour/ns) -68: Performance: 4.475 5.363 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.078 0.039 199.7 -68: (ns/day) (hour/ns) -68: Performance: 19.998 1.200 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (274 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.3 -68: (ns/day) (hour/ns) -68: Performance: 144.669 0.166 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 198.6 -68: (ns/day) (hour/ns) -68: Performance: 91.415 0.263 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.6 -68: (ns/day) (hour/ns) -68: Performance: 63.695 0.377 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (62 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.013 198.3 -68: (ns/day) (hour/ns) -68: Performance: 109.089 0.220 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.6 -68: (ns/day) (hour/ns) -68: Performance: 63.859 0.376 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.5 -68: (ns/day) (hour/ns) -68: Performance: 76.262 0.315 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (69 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 198.9 -68: (ns/day) (hour/ns) -68: Performance: 97.479 0.246 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.0 -68: (ns/day) (hour/ns) -68: Performance: 51.913 0.462 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.916 0.958 200.0 -68: (ns/day) (hour/ns) -68: Performance: 0.812 29.571 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (1027 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.097 0.048 199.7 -68: (ns/day) (hour/ns) -68: Performance: 30.319 0.792 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.125 0.063 199.7 -68: (ns/day) (hour/ns) -68: Performance: 12.410 1.934 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.5 -68: (ns/day) (hour/ns) -68: Performance: 69.616 0.345 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (519 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.016 198.8 -68: (ns/day) (hour/ns) -68: Performance: 92.889 0.258 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.059 0.030 199.4 -68: (ns/day) (hour/ns) -68: Performance: 26.309 0.912 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.044 0.022 199.2 -68: (ns/day) (hour/ns) -68: Performance: 35.422 0.678 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (137 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.060 0.030 199.4 -68: (ns/day) (hour/ns) -68: Performance: 48.695 0.493 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.047 0.023 199.2 -68: (ns/day) (hour/ns) -68: Performance: 33.307 0.721 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 198.3 -68: (ns/day) (hour/ns) -68: Performance: 73.992 0.324 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (205 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.8 -68: (ns/day) (hour/ns) -68: Performance: 115.063 0.209 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.7 -68: (ns/day) (hour/ns) -68: Performance: 64.456 0.372 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.7 -68: (ns/day) (hour/ns) -68: Performance: 69.632 0.345 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (104 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 198.8 -68: (ns/day) (hour/ns) -68: Performance: 100.732 0.238 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.012 199.0 -68: (ns/day) (hour/ns) -68: Performance: 62.441 0.384 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 199.1 -68: (ns/day) (hour/ns) -68: Performance: 61.688 0.389 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (123 ms) -68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (3593 ms total) -68: -68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.6 -68: (ns/day) (hour/ns) -68: Performance: 147.122 0.163 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 197.7 -68: (ns/day) (hour/ns) -68: Performance: 68.174 0.352 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.6 -68: (ns/day) (hour/ns) -68: Performance: 65.341 0.367 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (66 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 198.8 -68: (ns/day) (hour/ns) -68: Performance: 114.411 0.210 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.015 198.7 -68: (ns/day) (hour/ns) -68: Performance: 50.303 0.477 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.015 199.0 -68: (ns/day) (hour/ns) -68: Performance: 50.339 0.477 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (164 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.037 0.018 199.5 -68: (ns/day) (hour/ns) -68: Performance: 79.868 0.300 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 199.5 -68: (ns/day) (hour/ns) -68: Performance: 44.291 0.542 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.036 0.018 198.9 -68: (ns/day) (hour/ns) -68: Performance: 43.510 0.552 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (84 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.5 -68: (ns/day) (hour/ns) -68: Performance: 96.289 0.249 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.038 0.019 199.6 -68: (ns/day) (hour/ns) -68: Performance: 40.614 0.591 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 198.8 -68: (ns/day) (hour/ns) -68: Performance: 48.188 0.498 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (79 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.9 -68: (ns/day) (hour/ns) -68: Performance: 116.416 0.206 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.820 0.410 199.9 -68: (ns/day) (hour/ns) -68: Performance: 1.895 12.663 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.033 0.017 198.7 -68: (ns/day) (hour/ns) -68: Performance: 47.064 0.510 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (482 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.028 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 105.223 0.228 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.070 0.035 199.4 -68: (ns/day) (hour/ns) -68: Performance: 22.214 1.080 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.079 0.039 199.6 -68: (ns/day) (hour/ns) -68: Performance: 19.739 1.216 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (216 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.016 199.1 -68: (ns/day) (hour/ns) -68: Performance: 93.744 0.256 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 198.3 -68: (ns/day) (hour/ns) -68: Performance: 51.953 0.462 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 56.726 0.423 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (84 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 198.5 -68: (ns/day) (hour/ns) -68: Performance: 99.267 0.242 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 198.7 -68: (ns/day) (hour/ns) -68: Performance: 51.323 0.468 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.0 -68: (ns/day) (hour/ns) -68: Performance: 51.715 0.464 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (90 ms) -68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1267 ms total) -68: -68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.3 -68: (ns/day) (hour/ns) -68: Performance: 98.203 0.244 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.9 -68: (ns/day) (hour/ns) -68: Performance: 85.750 0.280 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.7 -68: (ns/day) (hour/ns) -68: Performance: 68.805 0.349 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (200 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.1 -68: (ns/day) (hour/ns) -68: Performance: 131.423 0.183 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 199.0 -68: (ns/day) (hour/ns) -68: Performance: 99.804 0.240 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.0 -68: (ns/day) (hour/ns) -68: Performance: 73.543 0.326 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (42 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.094 0.047 199.7 -68: (ns/day) (hour/ns) -68: Performance: 31.059 0.773 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.7 -68: (ns/day) (hour/ns) -68: Performance: 64.720 0.371 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.0 -68: (ns/day) (hour/ns) -68: Performance: 87.745 0.274 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (84 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 139.778 0.172 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 197.8 -68: (ns/day) (hour/ns) -68: Performance: 68.486 0.350 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.014 199.3 -68: (ns/day) (hour/ns) -68: Performance: 56.964 0.421 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (50 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 199.2 -68: (ns/day) (hour/ns) -68: Performance: 100.690 0.238 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 199.4 -68: (ns/day) (hour/ns) -68: Performance: 64.939 0.370 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.014 198.7 -68: (ns/day) (hour/ns) -68: Performance: 57.295 0.419 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (55 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 199.5 -68: (ns/day) (hour/ns) -68: Performance: 82.588 0.291 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.014 199.4 -68: (ns/day) (hour/ns) -68: Performance: 54.137 0.443 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 56.881 0.422 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (59 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.250 0.125 199.9 -68: (ns/day) (hour/ns) -68: Performance: 11.749 2.043 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.043 0.022 199.5 -68: (ns/day) (hour/ns) -68: Performance: 35.723 0.672 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.1 -68: (ns/day) (hour/ns) -68: Performance: 68.981 0.348 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (174 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 129.740 0.185 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 68.098 0.352 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.1 -68: (ns/day) (hour/ns) -68: Performance: 51.799 0.463 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (54 ms) -68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (721 ms total) -68: -68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact -68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.0 -68: (ns/day) (hour/ns) -68: Performance: 144.571 0.166 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.8 -68: (ns/day) (hour/ns) -68: Performance: 81.385 0.295 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.7 -68: (ns/day) (hour/ns) -68: Performance: 79.063 0.304 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (44 ms) -68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.014 199.4 -68: (ns/day) (hour/ns) -68: Performance: 102.511 0.234 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.036 0.018 199.4 -68: (ns/day) (hour/ns) -68: Performance: 43.617 0.550 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.028 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 56.154 0.427 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (61 ms) -68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (105 ms total) -68: -68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 198.5 -68: (ns/day) (hour/ns) -68: Performance: 181.018 0.133 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.7 -68: (ns/day) (hour/ns) -68: Performance: 87.491 0.274 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 78.088 0.307 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (40 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 198.7 -68: (ns/day) (hour/ns) -68: Performance: 177.110 0.136 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.008 198.5 -68: (ns/day) (hour/ns) -68: Performance: 102.990 0.233 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 198.6 -68: (ns/day) (hour/ns) -68: Performance: 111.718 0.215 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (34 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 198.5 -68: (ns/day) (hour/ns) -68: Performance: 212.985 0.113 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.007 198.5 -68: (ns/day) (hour/ns) -68: Performance: 103.853 0.231 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.0 -68: (ns/day) (hour/ns) -68: Performance: 77.690 0.309 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (35 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 198.5 -68: (ns/day) (hour/ns) -68: Performance: 201.577 0.119 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.013 0.007 197.5 -68: (ns/day) (hour/ns) -68: Performance: 115.178 0.208 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 198.3 -68: (ns/day) (hour/ns) -68: Performance: 88.258 0.272 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (35 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 199.0 -68: (ns/day) (hour/ns) -68: Performance: 123.712 0.194 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 72.733 0.330 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.5 -68: (ns/day) (hour/ns) -68: Performance: 87.136 0.275 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (43 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.1 -68: (ns/day) (hour/ns) -68: Performance: 144.010 0.167 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.1 -68: (ns/day) (hour/ns) -68: Performance: 83.957 0.286 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 198.5 -68: (ns/day) (hour/ns) -68: Performance: 73.985 0.324 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (42 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 199.1 -68: (ns/day) (hour/ns) -68: Performance: 115.020 0.209 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.049 0.025 199.5 -68: (ns/day) (hour/ns) -68: Performance: 31.614 0.759 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.050 0.025 199.4 -68: (ns/day) (hour/ns) -68: Performance: 30.819 0.779 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (77 ms) -68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (309 ms total) -68: -68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact -68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: MTTK coupling is deprecated and will soon be removed -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: MTTK coupling is deprecated and will soon be removed -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.014 199.2 -68: (ns/day) (hour/ns) -68: Performance: 108.086 0.222 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 199.0 -68: (ns/day) (hour/ns) -68: Performance: 65.505 0.366 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.5 -68: (ns/day) (hour/ns) -68: Performance: 61.649 0.389 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (51 ms) -68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (51 ms total) -68: -68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact -68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.036 0.018 199.2 -68: (ns/day) (hour/ns) -68: Performance: 81.082 0.296 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.012 198.6 -68: (ns/day) (hour/ns) -68: Performance: 65.820 0.365 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 199.0 -68: (ns/day) (hour/ns) -68: Performance: 43.951 0.546 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (64 ms) -68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.122 0.561 200.0 -68: (ns/day) (hour/ns) -68: Performance: 2.618 9.168 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.273 0.136 199.9 -68: (ns/day) (hour/ns) -68: Performance: 5.700 4.211 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.769 0.384 200.0 -68: (ns/day) (hour/ns) -68: Performance: 2.023 11.866 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1103 ms) -68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (1168 ms total) -68: -68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact -68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: Setting the AWH bias MC random seed to -537431810 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Setting the AWH bias MC random seed to -11535367 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.318 0.159 199.8 -68: (ns/day) (hour/ns) -68: Performance: 9.225 2.602 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.888 0.444 199.9 -68: (ns/day) (hour/ns) -68: Performance: 1.750 13.715 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.045 0.023 198.3 -68: (ns/day) (hour/ns) -68: Performance: 34.048 0.705 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (708 ms) -68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: Setting the AWH bias MC random seed to -17074180 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Setting the AWH bias MC random seed to 1070854119 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 198.1 -68: (ns/day) (hour/ns) -68: Performance: 85.607 0.280 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 196.9 -68: (ns/day) (hour/ns) -68: Performance: 52.972 0.453 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 197.6 -68: (ns/day) (hour/ns) -68: Performance: 47.360 0.507 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (100 ms) -68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (808 ms total) -68: -68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact -68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.061 0.031 199.7 -68: (ns/day) (hour/ns) -68: Performance: 47.689 0.503 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.3 -68: (ns/day) (hour/ns) -68: Performance: 51.424 0.467 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.037 0.019 198.6 -68: (ns/day) (hour/ns) -68: Performance: 41.985 0.572 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (105 ms) -68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (106 ms total) -68: -68: [----------] 3 tests from Checking/InitialConstraintsTest -68: [ RUN ] Checking/InitialConstraintsTest.Works/0 -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -1084229633 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 198.5 -68: (ns/day) (hour/ns) -68: Performance: 20.094 1.194 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (15 ms) -68: [ RUN ] Checking/InitialConstraintsTest.Works/1 -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -1074143780 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 199.0 -68: (ns/day) (hour/ns) -68: Performance: 22.168 1.083 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (14 ms) -68: [ RUN ] Checking/InitialConstraintsTest.Works/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: Integrator method md-vv-avek is implemented primarily for validation -68: purposes; for molecular dynamics, you should probably be using md or -68: md-vv -68: -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -1149899271 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 198.6 -68: (ns/day) (hour/ns) -68: Performance: 15.053 1.594 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (18 ms) -68: [----------] 3 tests from Checking/InitialConstraintsTest (48 ms total) -68: -68: [----------] Global test environment tear-down -68: [==========] 76 tests from 13 test suites ran. (9140 ms total) -68: [ PASSED ] 76 tests. -68/92 Test #68: MdrunIOTests .............................. Passed 9.16 sec -test 69 - Start 69: MdrunTestsOneRank - -69: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" -69: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -69: Test timeout computed to be: 600 -69: [==========] Running 29 tests from 8 test suites. -69: [----------] Global test environment set-up. -69: [----------] 1 test from CompelTest -69: [ RUN ] CompelTest.SwapCanRun -69: Generating 1-4 interactions: fudge = 0.5 -69: Split0 group 'Ch0' contains 83 atoms. -69: Split1 group 'Ch1' contains 83 atoms. -69: Solvent group 'SOL' contains 11931 atoms. -69: Swap group 'NA+' contains 19 atoms. -69: Swap group 'CL-' contains 19 atoms. -69: Number of degrees of freedom in T-Coupling group System is 27869.00 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -69: Removing center of mass motion in the presence of position restraints -69: might cause artifacts. When you are using position restraints to -69: equilibrate a macro-molecule, the artifacts are usually negligible. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Update groups can not be used for this system because there are three or more consecutively coupled constraints -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: SWAP: Determining initial numbers of ions per compartment. -69: SWAP: Setting pointers for checkpoint writing -69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -69: starting mdrun 'Channel_coco in octane membrane' -69: 2 steps, 0.0 ps. -69: Setting the LD random seed to -304637531 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: turning all bonds into constraints... -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: turning all bonds into constraints... -69: -69: Excluding 1 bonded neighbours molecule type 'NA' -69: -69: turning all bonds into constraints... -69: -69: Excluding 1 bonded neighbours molecule type 'CL' -69: -69: turning all bonds into constraints... -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning all bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -69: -69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 1 Mb of data -69: -69: Writing final coordinates. -69: -69: NOTE: 32 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.239 0.120 199.9 -69: (ns/day) (hour/ns) -69: Performance: 10.839 2.214 -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -69: -69: Update groups can not be used for this system because there are three or more consecutively coupled constraints -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: SWAP: Setting pointers for checkpoint writing -69: SWAP: Copying channel fluxes from checkpoint file data -69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -69: starting mdrun 'Channel_coco in octane membrane' -69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -69: -69: Writing final coordinates. -69: -69: NOTE: 24 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.148 0.074 199.8 -69: (ns/day) (hour/ns) -69: Performance: 17.466 1.374 -69: [ OK ] CompelTest.SwapCanRun (507 ms) -69: [----------] 1 test from CompelTest (507 ms total) -69: -69: [----------] 6 tests from BondedInteractionsTest -69: [ RUN ] BondedInteractionsTest.NormalBondWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 2 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 26 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.000 0.000 187.9 -69: (ns/day) (hour/ns) -69: Performance: 352.175 0.068 -69: Setting the LD random seed to 1390736063 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalBondWorks (7 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 2 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 25 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 186.1 -69: (ns/day) (hour/ns) -69: Performance: 271.248 0.088 -69: Setting the LD random seed to -1620067585 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) -69: [ RUN ] BondedInteractionsTest.NormalAngleWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 23 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 186.2 -69: (ns/day) (hour/ns) -69: Performance: 287.154 0.084 -69: Setting the LD random seed to -146801799 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalAngleWorks (5 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 24 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 184.7 -69: (ns/day) (hour/ns) -69: Performance: 301.487 0.080 -69: Setting the LD random seed to -609357313 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (5 ms) -69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 22 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 187.3 -69: (ns/day) (hour/ns) -69: Performance: 262.410 0.091 -69: Setting the LD random seed to 2104473957 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 22 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 187.3 -69: (ns/day) (hour/ns) -69: Performance: 271.046 0.089 -69: Setting the LD random seed to -16877569 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (5 ms) -69: [----------] 6 tests from BondedInteractionsTest (35 ms total) -69: -69: [----------] 2 tests from BoxDeformationTest -69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Argon' -69: 0 steps, 0.0 ps. -69: -69: NOTE: 29 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 165.9 -69: (ns/day) (hour/ns) -69: Performance: 572.493 0.042 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1610022907 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: Setting gen_seed to -7377229 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (6 ms) -69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 1293.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 20 steps, 0.0 ps. -69: Setting the LD random seed to -8388613 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -69: -69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.20 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.046 0.023 199.3 -69: (ns/day) (hour/ns) -69: Performance: 158.319 0.152 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (252 ms) -69: [----------] 2 tests from BoxDeformationTest (259 ms total) -69: -69: [----------] 1 test from PositionRestraintCommTest -69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: You have set rlist larger than the interaction cut-off, but you also have -69: verlet-buffer-tolerance > 0. Will set rlist using -69: verlet-buffer-tolerance. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: 13489 atoms are not part of any of the VCM groups -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: 13489 atoms are not part of any center of mass motion removal group. -69: This may lead to artifacts. -69: In most cases one should use one group for the whole system. -69: -69: Number of degrees of freedom in T-Coupling group System is 29527.73 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: Removing center of mass motion in the presence of position restraints -69: might cause artifacts. When you are using position restraints to -69: equilibrate a macro-molecule, the artifacts are usually negligible. -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Channel_coco in octane membrane' -69: 10 steps, 0.0 ps. -69: Setting the LD random seed to 1973386486 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 1 bonded neighbours molecule type 'NA' -69: -69: Excluding 1 bonded neighbours molecule type 'CL' -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: Chain0: 2.207 2.168 7.330 -69: Chain1: 2.228 2.186 2.401 -69: Chain0: 2.207 2.168 7.330 -69: Chain1: 2.228 2.186 2.401 -69: -69: This run will generate roughly 1 Mb of data -69: -69: Writing final coordinates. -69: -69: NOTE: 14 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.206 0.103 199.8 -69: (ns/day) (hour/ns) -69: Performance: 18.469 1.299 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (395 ms) -69: [----------] 1 test from PositionRestraintCommTest (395 ms total) -69: -69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to 1987829658 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.076 0.038 199.6 -69: (ns/day) (hour/ns) -69: Performance: 11.369 2.111 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -40477441 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.022 0.011 198.0 -69: (ns/day) (hour/ns) -69: Performance: 39.490 0.608 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) -69: -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (393 ms) -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -1903743813 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.023 0.011 198.5 -69: (ns/day) (hour/ns) -69: Performance: 38.040 0.631 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -69: Can not increase nstlist because an NVE ensemble is used -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to 1049213945 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.019 0.010 198.1 -69: (ns/day) (hour/ns) -69: Performance: 44.336 0.541 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (53 ms) -69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (447 ms total) -69: -69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Pull group 1 'FirstWaterMolecule' has 3 atoms -69: Pull group 2 'SecondWaterMolecule' has 3 atoms -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Pull group natoms pbc atom distance at start reference at t=0 -69: 1 3 2 -69: 2 3 5 1.112 nm 1.000 nm -69: -69: There was 1 NOTE -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -1427910721 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.038 0.019 199.1 -69: (ns/day) (hour/ns) -69: Performance: 22.926 1.047 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Pull group 1 'FirstWaterMolecule' has 3 atoms -69: Pull group 2 'SecondWaterMolecule' has 3 atoms -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Pull group natoms pbc atom distance at start reference at t=0 -69: 1 3 2 -69: 2 3 5 1.112 nm 1.000 nm -69: -69: There was 1 NOTE -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -69: Can not increase nstlist because an NVE ensemble is used -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to 1001958271 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.028 0.014 198.8 -69: (ns/day) (hour/ns) -69: Performance: 31.048 0.773 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (46 ms) -69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (46 ms total) -69: -69: [----------] 12 tests from FreezeWorks/FreezeGroupTest -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.025 0.012 198.8 -69: (ns/day) (hour/ns) -69: Performance: 62.918 0.381 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (22 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.020 0.010 198.5 -69: (ns/day) (hour/ns) -69: Performance: 78.801 0.305 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (20 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.254 0.127 199.8 -69: (ns/day) (hour/ns) -69: Performance: 6.128 3.916 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (137 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.027 0.013 198.9 -69: (ns/day) (hour/ns) -69: Performance: 57.811 0.415 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (24 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.017 0.008 197.5 -69: (ns/day) (hour/ns) -69: Performance: 91.982 0.261 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (20 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped -69: Parrinello-Rahman is not implemented in md-vv. -69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.015 0.008 197.9 -69: (ns/day) (hour/ns) -69: Performance: 99.905 0.240 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (21 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.034 0.017 198.7 -69: (ns/day) (hour/ns) -69: Performance: 45.141 0.532 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (31 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.021 0.011 198.5 -69: (ns/day) (hour/ns) -69: Performance: 73.147 0.328 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (26 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.024 0.012 198.6 -69: (ns/day) (hour/ns) -69: Performance: 64.552 0.372 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (42 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.020 0.010 197.8 -69: (ns/day) (hour/ns) -69: Performance: 76.734 0.313 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (39 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.049 0.025 199.4 -69: (ns/day) (hour/ns) -69: Performance: 31.408 0.764 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (59 ms) -69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (447 ms total) -69: -69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -478806785 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.016 0.008 198.6 -69: (ns/day) (hour/ns) -69: Performance: 193.262 0.124 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (14 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because verlet-buffer-tolerance is not set or used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -1029860109 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.017 0.009 198.2 -69: (ns/day) (hour/ns) -69: Performance: 180.642 0.133 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (16 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -1343556177 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.017 0.009 198.1 -69: (ns/day) (hour/ns) -69: Performance: 181.547 0.132 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (15 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because verlet-buffer-tolerance is not set or used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -350228514 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.018 0.009 198.6 -69: (ns/day) (hour/ns) -69: Performance: 174.397 0.138 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (14 ms) -69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (60 ms total) -69: -69: [----------] Global test environment tear-down -69: [==========] 29 tests from 8 test suites ran. (2479 ms total) -69: [ PASSED ] 28 tests. -69: [ SKIPPED ] 1 test, listed below: -69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -69/92 Test #69: MdrunTestsOneRank ......................... Passed 2.49 sec -test 70 - Start 70: MdrunTestsTwoRanks - -70: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" -70: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -70: Test timeout computed to be: 600 -70: [==========] Running 29 tests from 8 test suites. -70: [----------] Global test environment set-up. -70: [----------] 1 test from CompelTest -70: [ RUN ] CompelTest.SwapCanRun -70: Generating 1-4 interactions: fudge = 0.5 -70: Split0 group 'Ch0' contains 83 atoms. -70: Split1 group 'Ch1' contains 83 atoms. -70: Solvent group 'SOL' contains 11931 atoms. -70: Swap group 'NA+' contains 19 atoms. -70: Swap group 'CL-' contains 19 atoms. -70: Number of degrees of freedom in T-Coupling group System is 27869.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -70: Removing center of mass motion in the presence of position restraints -70: might cause artifacts. When you are using position restraints to -70: equilibrate a macro-molecule, the artifacts are usually negligible. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because there are three or more consecutively coupled constraints -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: SWAP: Determining initial numbers of ions per compartment. -70: SWAP: Setting pointers for checkpoint writing -70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -70: starting mdrun 'Channel_coco in octane membrane' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to 1035858359 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: turning all bonds into constraints... -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: turning all bonds into constraints... -70: -70: Excluding 1 bonded neighbours molecule type 'NA' -70: -70: turning all bonds into constraints... -70: -70: Excluding 1 bonded neighbours molecule type 'CL' -70: -70: turning all bonds into constraints... -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 1 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 2.4%. -70: The balanceable part of the MD step is 19%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 0.5%. -70: -70: -70: NOTE: 7 % of the run time was spent in domain decomposition, -70: 26 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.308 0.077 399.4 -70: (ns/day) (hour/ns) -70: Performance: 16.797 1.429 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -70: -70: Update groups can not be used for this system because there are three or more consecutively coupled constraints -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: SWAP: Setting pointers for checkpoint writing -70: SWAP: Copying channel fluxes from checkpoint file data -70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -70: starting mdrun 'Channel_coco in octane membrane' -70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: NOTE: 17 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.227 0.057 399.3 -70: (ns/day) (hour/ns) -70: Performance: 22.844 1.051 -70: [ OK ] CompelTest.SwapCanRun (462 ms) -70: [----------] 1 test from CompelTest (462 ms total) -70: -70: [----------] 6 tests from BondedInteractionsTest -70: [ RUN ] BondedInteractionsTest.NormalBondWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 2 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 14 % of the run time was spent in domain decomposition, -70: 9 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.001 382.3 -70: (ns/day) (hour/ns) -70: Performance: 155.899 0.154 -70: Setting the LD random seed to -37167112 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalBondWorks (7 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 2 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 18 % of the run time was spent in domain decomposition, -70: 16 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.000 381.2 -70: (ns/day) (hour/ns) -70: Performance: 174.813 0.137 -70: Setting the LD random seed to -1206532 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (1323 ms) -70: [ RUN ] BondedInteractionsTest.NormalAngleWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 21 % of the run time was spent in domain decomposition, -70: 16 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.001 381.3 -70: (ns/day) (hour/ns) -70: Performance: 172.279 0.139 -70: Setting the LD random seed to -37366017 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalAngleWorks (8 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 17 % of the run time was spent in domain decomposition, -70: 15 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.000 379.0 -70: (ns/day) (hour/ns) -70: Performance: 206.371 0.116 -70: Setting the LD random seed to -1074145719 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (9 ms) -70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 17 % of the run time was spent in domain decomposition, -70: 17 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.000 380.8 -70: (ns/day) (hour/ns) -70: Performance: 190.982 0.126 -70: Setting the LD random seed to -436602921 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (7 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 21 % of the run time was spent in domain decomposition, -70: 15 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.001 0.000 380.4 -70: (ns/day) (hour/ns) -70: Performance: 250.701 0.096 -70: Setting the LD random seed to -587203713 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (8 ms) -70: [----------] 6 tests from BondedInteractionsTest (1365 ms total) -70: -70: [----------] 2 tests from BoxDeformationTest -70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Number of degrees of freedom in T-Coupling group rest is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 0 steps, 0.0 ps. -70: -70: NOTE: 24 % of the run time was spent in domain decomposition, -70: 20 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.001 0.000 294.5 -70: (ns/day) (hour/ns) -70: Performance: 600.228 0.040 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -22954753 -70: -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Setting gen_seed to 1987633111 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (8 ms) -70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group rest is 1293.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 20 steps, 0.0 ps. -70: Setting the LD random seed to 1859846140 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -70: -70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.20 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 5.4%. -70: The balanceable part of the MD step is 27%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 1.4%. -70: -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.110 0.028 398.8 -70: (ns/day) (hour/ns) -70: Performance: 131.508 0.182 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (286 ms) -70: [----------] 2 tests from BoxDeformationTest (295 ms total) -70: -70: [----------] 1 test from PositionRestraintCommTest -70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: You have set rlist larger than the interaction cut-off, but you also have -70: verlet-buffer-tolerance > 0. Will set rlist using -70: verlet-buffer-tolerance. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: 13489 atoms are not part of any of the VCM groups -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: 13489 atoms are not part of any center of mass motion removal group. -70: This may lead to artifacts. -70: In most cases one should use one group for the whole system. -70: -70: Number of degrees of freedom in T-Coupling group System is 29527.73 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: Removing center of mass motion in the presence of position restraints -70: might cause artifacts. When you are using position restraints to -70: equilibrate a macro-molecule, the artifacts are usually negligible. -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Channel_coco in octane membrane' -70: 10 steps, 0.0 ps. -70: Setting the LD random seed to -1082952358 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 1 bonded neighbours molecule type 'NA' -70: -70: Excluding 1 bonded neighbours molecule type 'CL' -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: Chain0: 2.207 2.168 7.330 -70: Chain1: 2.228 2.186 2.401 -70: Chain0: 2.207 2.168 7.330 -70: Chain1: 2.228 2.186 2.401 -70: -70: This run will generate roughly 1 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 11 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: NOTE: 18 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.345 0.086 399.5 -70: (ns/day) (hour/ns) -70: Performance: 22.006 1.091 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1277 ms) -70: [----------] 1 test from PositionRestraintCommTest (1278 ms total) -70: -70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to 1742993407 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 40 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.033 0.008 395.6 -70: (ns/day) (hour/ns) -70: Performance: 51.575 0.465 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to 469729193 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 42 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.027 0.007 396.4 -70: (ns/day) (hour/ns) -70: Performance: 62.576 0.384 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) -70: -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (358 ms) -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to 1073592823 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 39 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.034 0.009 395.1 -70: (ns/day) (hour/ns) -70: Performance: 50.407 0.476 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -70: Can not increase nstlist because an NVE ensemble is used -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -43265036 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 43 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.031 0.008 395.4 -70: (ns/day) (hour/ns) -70: Performance: 55.840 0.430 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (51 ms) -70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (410 ms total) -70: -70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -1375749145 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 48 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.058 0.015 397.4 -70: (ns/day) (hour/ns) -70: Performance: 29.631 0.810 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -70: Can not increase nstlist because an NVE ensemble is used -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -1089736711 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 48 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.046 0.012 396.7 -70: (ns/day) (hour/ns) -70: Performance: 37.448 0.641 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (43 ms) -70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (43 ms total) -70: -70: [----------] 12 tests from FreezeWorks/FreezeGroupTest -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 14.4%. -70: The balanceable part of the MD step is 39%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 5.6%. -70: -70: NOTE: 5.6 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.041 0.010 396.7 -70: (ns/day) (hour/ns) -70: Performance: 74.677 0.321 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (24 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 21.4%. -70: The balanceable part of the MD step is 21%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 4.5%. -70: -70: -70: NOTE: 39 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.032 0.008 395.5 -70: (ns/day) (hour/ns) -70: Performance: 97.594 0.246 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (19 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 20.9%. -70: The balanceable part of the MD step is 44%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 9.3%. -70: -70: NOTE: 9.3 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 50 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 1.043 0.261 399.9 -70: (ns/day) (hour/ns) -70: Performance: 2.982 8.049 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (271 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 11.1%. -70: The balanceable part of the MD step is 46%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 5.2%. -70: -70: NOTE: 5.2 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.040 0.010 394.7 -70: (ns/day) (hour/ns) -70: Performance: 76.952 0.312 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (22 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 10.3%. -70: The balanceable part of the MD step is 51%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 5.3%. -70: -70: NOTE: 5.3 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 39 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.031 0.008 382.5 -70: (ns/day) (hour/ns) -70: Performance: 95.961 0.250 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (19 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped -70: Parrinello-Rahman is not implemented in md-vv. -70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.032 0.008 397.0 -70: (ns/day) (hour/ns) -70: Performance: 96.260 0.249 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (23 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 43 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.032 0.008 397.7 -70: (ns/day) (hour/ns) -70: Performance: 95.367 0.252 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (21 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 42 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.030 0.007 397.4 -70: (ns/day) (hour/ns) -70: Performance: 104.669 0.229 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (21 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.036 0.009 397.3 -70: (ns/day) (hour/ns) -70: Performance: 84.706 0.283 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (37 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.054 0.013 397.7 -70: (ns/day) (hour/ns) -70: Performance: 57.717 0.416 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (42 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.036 0.009 397.4 -70: (ns/day) (hour/ns) -70: Performance: 86.722 0.277 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (40 ms) -70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (544 ms total) -70: -70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -18089825 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 2.4%. -70: The balanceable part of the MD step is 37%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 0.9%. -70: -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.037 0.009 396.0 -70: (ns/day) (hour/ns) -70: Performance: 165.732 0.145 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (16 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because verlet-buffer-tolerance is not set or used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -286261282 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 1.8%. -70: The balanceable part of the MD step is 36%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 0.6%. -70: -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.026 0.007 394.6 -70: (ns/day) (hour/ns) -70: Performance: 232.296 0.103 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (12 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to 1992030167 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 8.6%. -70: The balanceable part of the MD step is 46%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 4.0%. -70: -70: -70: NOTE: 44 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.025 0.006 395.9 -70: (ns/day) (hour/ns) -70: Performance: 241.467 0.099 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (11 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because verlet-buffer-tolerance is not set or used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -83938309 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 1.9%. -70: The balanceable part of the MD step is 47%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 0.9%. -70: -70: -70: NOTE: 44 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.029 0.007 395.2 -70: (ns/day) (hour/ns) -70: Performance: 213.459 0.112 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (12 ms) -70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (53 ms total) -70: -70: [----------] Global test environment tear-down -70: [==========] 29 tests from 8 test suites ran. (4774 ms total) -70: [ PASSED ] 28 tests. -70: [ SKIPPED ] 1 test, listed below: -70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 4.79 sec -test 71 - Start 71: MdrunSingleRankAlgorithmsTests - -71: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" -71: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -71: Test timeout computed to be: 600 -71: [==========] Running 5 tests from 3 test suites. -71: [----------] Global test environment set-up. -71: [----------] 1 test from DispersionCorrectionTest -71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun -71: Generating 1-4 interactions: fudge = 0.5 -71: Number of degrees of freedom in T-Coupling group System is 30.00 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -71: There are 9 non-linear virtual site constructions. Their contribution to -71: the energy error is approximated. In most cases this does not affect the -71: error significantly. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 2 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 -71: -71: Update groups can not be used for this system because an incompatible virtual site type is used -71: -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine dipeptide in vacuo' -71: 200 steps, 0.4 ps. -71: Setting the LD random seed to -18370829 -71: -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -71: -71: Cleaning up constraints and constant bonded interactions with virtual sites -71: -71: Converted 3 Bonds with virtual sites to connections, 7 left -71: -71: Removed 18 Angles with virtual sites, 21 left -71: -71: Removed 10 Proper Dih.s with virtual sites, 44 left -71: -71: Converted 12 Constraints with virtual sites to connections, 0 left -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -71: -71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.029 0.015 199.1 -71: (ns/day) (hour/ns) -71: Performance: 2367.778 0.010 -71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (39 ms) -71: [----------] 1 test from DispersionCorrectionTest (39 ms total) -71: -71: [----------] 1 test from OriresTest -71: [ RUN ] OriresTest.OriresCanRun -71: Generating 1-4 interactions: fudge = 0.5 -71: Number of degrees of freedom in T-Coupling group System is 518.00 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There was 1 NOTE -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. -71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 -71: -71: -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' -71: 10 steps, 0.0 ps. -71: Setting the LD random seed to -541851781 -71: -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/orires_1lvz.gro' -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -71: -71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.028 0.014 198.9 -71: (ns/day) (hour/ns) -71: Performance: 136.802 0.175 -71: [ OK ] OriresTest.OriresCanRun (307 ms) -71: [----------] 1 test from OriresTest (307 ms total) -71: -71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 -71: Number of degrees of freedom in T-Coupling group rest is 10.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 2 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Dipoles' -71: 20 steps, 0.1 ps. -71: Setting the LD random seed to -71827617 -71: -71: Generated 1 of the 1 non-bonded parameter combinations -71: -71: Excluding 1 bonded neighbours molecule type 'Dipole' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -71: -71: Searching the wall atom type(s) -71: -71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 -71: -71: Estimate for the relative computational load of the PME mesh part: 1.00 -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.031 0.016 198.9 -71: (ns/day) (hour/ns) -71: Performance: 288.959 0.083 -71: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) -71: -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (612 ms) -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 -71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. -71: The supported numbers are > 1. -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: With epsilon_surface > 0 all molecules should be neutral. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: With epsilon_surface > 0 you can only use domain decomposition when there -71: are only small molecules with all bonds constrained (mdrun will check for -71: this). -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 4 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Dipoles' -71: 20 steps, 0.1 ps. -71: Setting the LD random seed to 2147448315 -71: -71: Generated 1 of the 1 non-bonded parameter combinations -71: -71: Excluding 1 bonded neighbours molecule type 'Dipole' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -71: -71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 -71: -71: Estimate for the relative computational load of the PME mesh part: 1.00 -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.022 0.011 198.8 -71: (ns/day) (hour/ns) -71: Performance: 404.804 0.059 -71: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (221 ms) -71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (833 ms total) -71: -71: [----------] Global test environment tear-down -71: [==========] 5 tests from 3 test suites ran. (1331 ms total) -71: [ PASSED ] 5 tests. -71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 1.34 sec -test 72 - Start 72: Minimize1RankTests - -72: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/Minimize1RankTests.xml" -72: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -72: Test timeout computed to be: 600 -72: [==========] Running 12 tests from 2 test suites. -72: [----------] Global test environment set-up. -72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -4.7991062e+01 -72: Maximum force = 1.8629750e+02 on atom 13 -72: Norm of force = 8.7721970e+01 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (228 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 3.02330e+02 on atom 3 -72: F-Norm = 1.18024e+02 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -5.5862370e+01 -72: Maximum force = 4.2727301e+02 on atom 13 -72: Norm of force = 1.8452934e+02 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (232 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 22.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 3.1937723e+02 -72: Maximum force = 9.9988623e+03 on atom 9 -72: Norm of force = 4.6166987e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: turning H bonds into constraints... -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (54 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: -72: NOTE 3 [file glycine_vacuo.top, line 12]: -72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -72: -72: Number of degrees of freedom in T-Coupling group System is 22.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 5 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 2.41575e+04 on atom 10 -72: F-Norm = 1.18451e+04 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 1.5174393e+02 -72: Maximum force = 7.4208867e+03 on atom 9 -72: Norm of force = 3.5693011e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: turning H bonds into constraints... -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (56 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: NOTE 3 [file unknown]: -72: You are using constraints on all bonds, whereas the forcefield has been -72: parametrized only with constraints involving hydrogen atoms. We suggest -72: using constraints = h-bonds instead, this will also improve performance. -72: -72: Number of degrees of freedom in T-Coupling group System is 23.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 5 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Update groups can not be used for this system because an incompatible virtual site type is used -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -1.5698462e+02 -72: Maximum force = 4.5704999e+02 on atom 17 -72: Norm of force = 1.8327331e+02 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -72: -72: turning all bonds into constraints... -72: -72: Cleaning up constraints and constant bonded interactions with virtual sites -72: -72: Removed 18 Angles with virtual sites, 21 left -72: -72: Removed 10 Proper Dih.s with virtual sites, 44 left -72: -72: Converted 15 Constraints with virtual sites to connections, 7 left -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (10 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: NOTE 3 [file unknown]: -72: You are using constraints on all bonds, whereas the forcefield has been -72: parametrized only with constraints involving hydrogen atoms. We suggest -72: using constraints = h-bonds instead, this will also improve performance. -72: -72: -72: NOTE 4 [file unknown]: -72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -72: -72: Number of degrees of freedom in T-Coupling group System is 23.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 6 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Update groups can not be used for this system because an incompatible virtual site type is used -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 1.06799e+03 on atom 28 -72: F-Norm = 4.26916e+02 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -1.6941089e+02 -72: Maximum force = 2.1831544e+02 on atom 17 -72: Norm of force = 7.9209568e+01 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -72: -72: turning all bonds into constraints... -72: -72: Cleaning up constraints and constant bonded interactions with virtual sites -72: -72: Removed 18 Angles with virtual sites, 21 left -72: -72: Removed 10 Proper Dih.s with virtual sites, 44 left -72: -72: Converted 15 Constraints with virtual sites to connections, 7 left -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (13 ms) -72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (596 ms total) -72: -72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents converged to Fmax < 10 in 1 steps -72: Potential Energy = -9.7425687e-01 -72: Maximum force = 4.0132279e+00 on atom 1 -72: Norm of force = 1.6383933e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (7 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 4.01323e+00 on atom 1 -72: F-Norm = 1.63839e+00 -72: -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -72: Potential Energy = -9.9064195e-01 -72: Maximum force = 2.5781672e+00 on atom 1 -72: Norm of force = 1.0525324e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (5 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Low-Memory BFGS Minimizer: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: Using 10 BFGS correction steps. -72: -72: F-max = 4.01323e+00 on atom 1 -72: F-Norm = 1.63839e+00 -72: -72: -72: writing lowest energy coordinates. -72: -72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps -72: Potential Energy = -9.9064195e-01 -72: Maximum force = 2.5781672e+00 on atom 1 -72: Norm of force = 1.0525324e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 3.1939685e+02 -72: Maximum force = 9.9704248e+03 on atom 9 -72: Norm of force = 4.6227543e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (55 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 2.41672e+04 on atom 10 -72: F-Norm = 1.19357e+04 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 1.5625757e+02 -72: Maximum force = 7.5018242e+03 on atom 9 -72: Norm of force = 3.6139019e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (56 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Low-Memory BFGS Minimizer: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: Using 10 BFGS correction steps. -72: -72: F-max = 2.41672e+04 on atom 10 -72: F-Norm = 1.19357e+04 -72: -72: -72: Energy minimization has stopped, but the forces have not converged to the -72: requested precision Fmax < 10 (which may not be possible for your system). It -72: stopped because the algorithm tried to make a new step whose size was too -72: small, or there was no change in the energy since last step. Either way, we -72: regard the minimization as converged to within the available machine -72: precision, given your starting configuration and EM parameters. -72: -72: Double precision normally gives you higher accuracy, but this is often not -72: needed for preparing to run molecular dynamics. -72: -72: writing lowest energy coordinates. -72: -72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, -72: but did not reach the requested Fmax < 10. -72: Potential Energy = 5.6111725e+02 -72: Maximum force = 1.2685490e+04 on atom 10 -72: Norm of force = 6.0643616e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (57 ms) -72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (188 ms total) -72: -72: [----------] Global test environment tear-down -72: [==========] 12 tests from 2 test suites ran. (882 ms total) -72: [ PASSED ] 12 tests. -72/92 Test #72: Minimize1RankTests ........................ Passed 0.90 sec -test 73 - Start 73: Minimize2RankTests - -73: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/Minimize2RankTests.xml" -73: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -73: Test timeout computed to be: 600 -73: [==========] Running 12 tests from 2 test suites. -73: [----------] Global test environment set-up. -73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -4.7990963e+01 -73: Maximum force = 1.8629601e+02 on atom 13 -73: Norm of force = 8.7721907e+01 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -73: -73: Generated 330891 of the 330891 1-4 parameter combinations -73: -73: Excluding 2 bonded neighbours molecule type 'SOL' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (233 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 3.02331e+02 on atom 3 -73: F-Norm = 1.18024e+02 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -5.5862366e+01 -73: Maximum force = 4.2726111e+02 on atom 13 -73: Norm of force = 1.8452509e+02 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -73: -73: Generated 330891 of the 330891 1-4 parameter combinations -73: -73: Excluding 2 bonded neighbours molecule type 'SOL' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (225 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 22.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 3.1937720e+02 -73: Maximum force = 9.9988643e+03 on atom 9 -73: Norm of force = 4.6166993e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: turning H bonds into constraints... -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (58 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: -73: NOTE 3 [file glycine_vacuo.top, line 12]: -73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -73: -73: Number of degrees of freedom in T-Coupling group System is 22.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 5 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 2.41575e+04 on atom 10 -73: F-Norm = 1.18451e+04 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 1.5174432e+02 -73: Maximum force = 7.4208867e+03 on atom 9 -73: Norm of force = 3.5692995e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: turning H bonds into constraints... -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (56 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: -73: NOTE 3 [file unknown]: -73: You are using constraints on all bonds, whereas the forcefield has been -73: parametrized only with constraints involving hydrogen atoms. We suggest -73: using constraints = h-bonds instead, this will also improve performance. -73: -73: Number of degrees of freedom in T-Coupling group System is 23.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 5 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Update groups can not be used for this system because an incompatible virtual site type is used -73: -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -1.5698450e+02 -73: Maximum force = 4.5703549e+02 on atom 17 -73: Norm of force = 1.8327631e+02 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -73: -73: turning all bonds into constraints... -73: -73: Cleaning up constraints and constant bonded interactions with virtual sites -73: -73: Removed 18 Angles with virtual sites, 21 left -73: -73: Removed 10 Proper Dih.s with virtual sites, 44 left -73: -73: Converted 15 Constraints with virtual sites to connections, 7 left -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (11 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: -73: NOTE 3 [file unknown]: -73: You are using constraints on all bonds, whereas the forcefield has been -73: parametrized only with constraints involving hydrogen atoms. We suggest -73: using constraints = h-bonds instead, this will also improve performance. -73: -73: -73: NOTE 4 [file unknown]: -73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -73: -73: Number of degrees of freedom in T-Coupling group System is 23.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 6 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Update groups can not be used for this system because an incompatible virtual site type is used -73: -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 1.06799e+03 on atom 28 -73: F-Norm = 4.26916e+02 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -1.6941107e+02 -73: Maximum force = 2.1831662e+02 on atom 17 -73: Norm of force = 7.9213110e+01 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -73: -73: turning all bonds into constraints... -73: -73: Cleaning up constraints and constant bonded interactions with virtual sites -73: -73: Removed 18 Angles with virtual sites, 21 left -73: -73: Removed 10 Proper Dih.s with virtual sites, 44 left -73: -73: Converted 15 Constraints with virtual sites to connections, 7 left -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (13 ms) -73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (599 ms total) -73: -73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents converged to Fmax < 10 in 1 steps -73: Potential Energy = -9.7425687e-01 -73: Maximum force = 4.0132279e+00 on atom 3 -73: Norm of force = 1.6383933e+00 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (9 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 4.01323e+00 on atom 3 -73: F-Norm = 1.63839e+00 -73: -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -73: Potential Energy = -9.9064195e-01 -73: Maximum force = 2.5781672e+00 on atom 3 -73: Norm of force = 1.0525324e+00 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (7 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: -73: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: -73: There was 1 WARNING -73: Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 3.1939673e+02 -73: Maximum force = 9.9704229e+03 on atom 9 -73: Norm of force = 4.6227558e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (55 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 2.41672e+04 on atom 10 -73: F-Norm = 1.19357e+04 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 1.5625764e+02 -73: Maximum force = 7.5018237e+03 on atom 9 -73: Norm of force = 3.6139019e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (70 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: -73: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: -73: There was 1 WARNING -73: Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (54 ms) -73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (200 ms total) -73: -73: [----------] Global test environment tear-down -73: [==========] 12 tests from 2 test suites ran. (893 ms total) -73: [ PASSED ] 12 tests. -73/92 Test #73: Minimize2RankTests ........................ Passed 0.91 sec -test 74 - Start 74: MdrunNonIntegratorTests - -74: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" -74: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -74: Test timeout computed to be: 600 -74: [==========] Running 46 tests from 3 test suites. -74: [----------] Global test environment set-up. -74: [----------] 1 test from NonbondedBenchTest -74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest -74: SIMD width: 4 -74: System size: 3000 atoms -74: Cut-off radius: 1 nm -74: Number of threads: 1 -74: Number of iterations: 1 -74: Compute energies: no -74: Ewald excl. corr.: analytical -74: -74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle -74: total useful -74: Ewald all geom. 4xM 10.345 10.3451 0.1151 0.0609 -74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (15 ms) -74: [----------] 1 test from NonbondedBenchTest (15 ms total) -74: -74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: NVE simulation: will use the initial temperature of 68.810 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.018 0.009 198.6 -74: (ns/day) (hour/ns) -74: Performance: 163.307 0.147 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' -74: -74: trr version: GMX_trn_file (single precision) -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 13 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 196.1 -74: (ns/day) (hour/ns) -74: Performance: 1290.447 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (19 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: NVE simulation: will use the initial temperature of 68.810 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.022 0.011 199.6 -74: (ns/day) (hour/ns) -74: Performance: 135.039 0.178 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 23 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 192.2 -74: (ns/day) (hour/ns) -74: Performance: 2773.793 0.009 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (19 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: There were 2 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.016 0.008 198.9 -74: (ns/day) (hour/ns) -74: Performance: 182.002 0.132 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 24 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 192.9 -74: (ns/day) (hour/ns) -74: Performance: 2401.791 0.010 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (16 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: There were 2 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.015 0.008 198.5 -74: (ns/day) (hour/ns) -74: Performance: 190.837 0.126 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 24 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.4 -74: (ns/day) (hour/ns) -74: Performance: 2225.648 0.011 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (15 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: NVE simulation: will use the initial temperature of 398.997 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.018 0.009 198.6 -74: (ns/day) (hour/ns) -74: Performance: 163.737 0.147 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 23 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 192.8 -74: (ns/day) (hour/ns) -74: Performance: 2477.119 0.010 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (240 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: NVE simulation: will use the initial temperature of 398.997 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.021 0.011 199.4 -74: (ns/day) (hour/ns) -74: Performance: 137.186 0.175 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 192.2 -74: (ns/day) (hour/ns) -74: Performance: 2491.142 0.010 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (228 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.026 0.013 199.2 -74: (ns/day) (hour/ns) -74: Performance: 111.919 0.214 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 27 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.000 193.5 -74: (ns/day) (hour/ns) -74: Performance: 3180.482 0.008 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (250 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.029 0.015 199.2 -74: (ns/day) (hour/ns) -74: Performance: 99.941 0.240 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 23 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 191.9 -74: (ns/day) (hour/ns) -74: Performance: 2315.142 0.010 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (252 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: NVE simulation: will use the initial temperature of 456.887 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 6 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.038 0.019 199.3 -74: (ns/day) (hour/ns) -74: Performance: 76.311 0.315 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 24 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 194.7 -74: (ns/day) (hour/ns) -74: Performance: 1506.626 0.016 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (45 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: NVE simulation: will use the initial temperature of 456.887 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 6 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.014 199.1 -74: (ns/day) (hour/ns) -74: Performance: 108.561 0.221 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 194.2 -74: (ns/day) (hour/ns) -74: Performance: 1613.566 0.015 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (28 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 5 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.026 0.013 198.5 -74: (ns/day) (hour/ns) -74: Performance: 111.901 0.214 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 46 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.005 0.002 196.4 -74: (ns/day) (hour/ns) -74: Performance: 638.470 0.038 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (108 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 5 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.014 198.7 -74: (ns/day) (hour/ns) -74: Performance: 106.402 0.226 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 193.9 -74: (ns/day) (hour/ns) -74: Performance: 1504.786 0.016 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (73 ms) -74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1300 ms total) -74: -74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 198.6 -74: (ns/day) (hour/ns) -74: Performance: 91.909 0.261 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 15 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 130.4 -74: (ns/day) (hour/ns) -74: Performance: 736.825 0.033 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (46 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 198.6 -74: (ns/day) (hour/ns) -74: Performance: 90.183 0.266 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 19 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 185.4 -74: (ns/day) (hour/ns) -74: Performance: 852.441 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (43 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.028 0.014 198.4 -74: (ns/day) (hour/ns) -74: Performance: 104.429 0.230 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 181.7 -74: (ns/day) (hour/ns) -74: Performance: 1043.461 0.023 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (37 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 198.6 -74: (ns/day) (hour/ns) -74: Performance: 89.949 0.267 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 180.9 -74: (ns/day) (hour/ns) -74: Performance: 1019.628 0.024 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (39 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 198.6 -74: (ns/day) (hour/ns) -74: Performance: 90.849 0.264 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 181.0 -74: (ns/day) (hour/ns) -74: Performance: 1000.259 0.024 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (40 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.064 0.032 199.3 -74: (ns/day) (hour/ns) -74: Performance: 45.900 0.523 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 19 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 184.1 -74: (ns/day) (hour/ns) -74: Performance: 909.447 0.026 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (56 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.028 0.014 198.4 -74: (ns/day) (hour/ns) -74: Performance: 105.627 0.227 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 183.6 -74: (ns/day) (hour/ns) -74: Performance: 1006.469 0.024 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (36 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.028 0.014 198.4 -74: (ns/day) (hour/ns) -74: Performance: 104.159 0.230 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 182.7 -74: (ns/day) (hour/ns) -74: Performance: 1028.480 0.023 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (36 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.013 198.4 -74: (ns/day) (hour/ns) -74: Performance: 109.145 0.220 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 185.1 -74: (ns/day) (hour/ns) -74: Performance: 1063.455 0.023 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (36 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.035 0.018 199.1 -74: (ns/day) (hour/ns) -74: Performance: 83.036 0.289 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 25 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 186.4 -74: (ns/day) (hour/ns) -74: Performance: 1422.113 0.017 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (33 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.024 0.012 199.0 -74: (ns/day) (hour/ns) -74: Performance: 120.359 0.199 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 183.7 -74: (ns/day) (hour/ns) -74: Performance: 1836.243 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (25 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.013 199.6 -74: (ns/day) (hour/ns) -74: Performance: 110.221 0.218 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 185.6 -74: (ns/day) (hour/ns) -74: Performance: 1907.895 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (26 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.041 0.020 199.6 -74: (ns/day) (hour/ns) -74: Performance: 71.717 0.335 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 183.0 -74: (ns/day) (hour/ns) -74: Performance: 1863.458 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (33 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.038 0.019 199.6 -74: (ns/day) (hour/ns) -74: Performance: 77.420 0.310 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 183.8 -74: (ns/day) (hour/ns) -74: Performance: 1824.820 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (32 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.034 0.017 199.5 -74: (ns/day) (hour/ns) -74: Performance: 84.956 0.282 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 18 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 184.0 -74: (ns/day) (hour/ns) -74: Performance: 1761.680 0.014 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (30 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.044 0.022 199.6 -74: (ns/day) (hour/ns) -74: Performance: 67.010 0.358 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 185.4 -74: (ns/day) (hour/ns) -74: Performance: 1795.045 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (35 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 199.5 -74: (ns/day) (hour/ns) -74: Performance: 97.084 0.247 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 183.4 -74: (ns/day) (hour/ns) -74: Performance: 1407.492 0.017 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (29 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.026 0.013 199.4 -74: (ns/day) (hour/ns) -74: Performance: 110.736 0.217 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 19 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 185.5 -74: (ns/day) (hour/ns) -74: Performance: 1343.641 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (28 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.031 0.016 199.5 -74: (ns/day) (hour/ns) -74: Performance: 93.585 0.256 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 180.0 -74: (ns/day) (hour/ns) -74: Performance: 1433.363 0.017 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (30 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.014 199.2 -74: (ns/day) (hour/ns) -74: Performance: 106.439 0.225 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 180.6 -74: (ns/day) (hour/ns) -74: Performance: 1362.662 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (29 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 199.5 -74: (ns/day) (hour/ns) -74: Performance: 96.102 0.250 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 178.4 -74: (ns/day) (hour/ns) -74: Performance: 1342.177 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (30 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.028 0.014 199.5 -74: (ns/day) (hour/ns) -74: Performance: 103.950 0.231 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 181.1 -74: (ns/day) (hour/ns) -74: Performance: 1359.354 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (29 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.014 199.1 -74: (ns/day) (hour/ns) -74: Performance: 107.174 0.224 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 181.6 -74: (ns/day) (hour/ns) -74: Performance: 1289.097 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (36 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.029 0.014 199.0 -74: (ns/day) (hour/ns) -74: Performance: 101.884 0.236 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 182.5 -74: (ns/day) (hour/ns) -74: Performance: 1785.679 0.013 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (39 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.182 0.091 199.8 -74: (ns/day) (hour/ns) -74: Performance: 16.135 1.487 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 179.7 -74: (ns/day) (hour/ns) -74: Performance: 1220.161 0.020 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (115 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.502 0.251 199.9 -74: (ns/day) (hour/ns) -74: Performance: 5.850 4.103 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 24 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 183.6 -74: (ns/day) (hour/ns) -74: Performance: 1161.500 0.021 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (274 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.022 0.011 198.8 -74: (ns/day) (hour/ns) -74: Performance: 134.684 0.178 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 179.0 -74: (ns/day) (hour/ns) -74: Performance: 1432.696 0.017 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (37 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.024 0.012 199.0 -74: (ns/day) (hour/ns) -74: Performance: 122.763 0.195 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 177.2 -74: (ns/day) (hour/ns) -74: Performance: 1336.934 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (34 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.023 0.012 199.1 -74: (ns/day) (hour/ns) -74: Performance: 127.104 0.189 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 181.7 -74: (ns/day) (hour/ns) -74: Performance: 1370.239 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (34 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.028 0.014 199.2 -74: (ns/day) (hour/ns) -74: Performance: 103.409 0.232 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 181.7 -74: (ns/day) (hour/ns) -74: Performance: 1359.354 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (36 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.031 0.016 199.2 -74: (ns/day) (hour/ns) -74: Performance: 93.334 0.257 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 179.9 -74: (ns/day) (hour/ns) -74: Performance: 1360.555 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (38 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 199.2 -74: (ns/day) (hour/ns) -74: Performance: 98.426 0.244 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 181.7 -74: (ns/day) (hour/ns) -74: Performance: 1355.466 0.018 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (37 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.033 0.016 199.2 -74: (ns/day) (hour/ns) -74: Performance: 89.532 0.268 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 180.9 -74: (ns/day) (hour/ns) -74: Performance: 1286.942 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (38 ms) -74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1494 ms total) -74: -74: [----------] Global test environment tear-down -74: [==========] 46 tests from 3 test suites ran. (2906 ms total) -74: [ PASSED ] 46 tests. -74/92 Test #74: MdrunNonIntegratorTests ................... Passed 2.92 sec -test 75 - Start 75: MdrunTpiTests - -75: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunTpiTests.xml" -75: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -75: Test timeout computed to be: 600 -75: [==========] Running 3 tests from 1 test suite. -75: [----------] Global test environment set-up. -75: [----------] 3 tests from Simple/TpiTest -75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (227 ms) -75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (210 ms) -75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (231 ms) -75: [----------] 3 tests from Simple/TpiTest (669 ms total) -75: -75: [----------] Global test environment tear-down -75: [==========] 3 tests from 1 test suite ran. (726 ms total) -75: [ PASSED ] 3 tests. -75/92 Test #75: MdrunTpiTests ............................. Passed 0.74 sec -test 76 - Start 76: MdrunMpiTests - -76: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMpiTests.xml" -76: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -76: Test timeout computed to be: 600 -76: [==========] Running 16 tests from 2 test suites. -76: [----------] Global test environment set-up. -76: [----------] 4 tests from MimicTest -76: [ RUN ] MimicTest.OneQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 23 % of the run time was spent in domain decomposition, -76: 13 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.000 375.8 -76: (ns/day) (hour/ns) -76: Performance: 249.064 0.096 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1750283145 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.OneQuantumMol (6 ms) -76: [ RUN ] MimicTest.AllQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 28 % of the run time was spent in domain decomposition, -76: 13 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.000 376.8 -76: (ns/day) (hour/ns) -76: Performance: 219.032 0.110 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 503308057 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.AllQuantumMol (5 ms) -76: [ RUN ] MimicTest.TwoQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 23 % of the run time was spent in domain decomposition, -76: 13 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.000 379.9 -76: (ns/day) (hour/ns) -76: Performance: 322.984 0.074 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -67119142 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.TwoQuantumMol (5 ms) -76: [ RUN ] MimicTest.BondCuts -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 66.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: NVE simulation: will use the initial temperature of 300.368 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -76: -76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 21 % of the run time was spent in domain decomposition, -76: 15 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.000 380.5 -76: (ns/day) (hour/ns) -76: Performance: 201.047 0.119 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -44040227 -76: -76: Generated 2211 of the 2211 non-bonded parameter combinations -76: -76: Generated 2211 of the 2211 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.BondCuts (11 ms) -76: [----------] 4 tests from MimicTest (29 ms total) -76: -76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 9.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: There was 1 NOTE -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 9.00 -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 9.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: The optimal PME mesh load for parallel simulations is below 0.5 -76: and for highly parallel simulations between 0.25 and 0.33, -76: for higher performance, increase the cut-off and the PME grid spacing. -76: -76: -76: -76: There were 2 NOTEs -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 9.00 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: The optimal PME mesh load for parallel simulations is below 0.5 -76: and for highly parallel simulations between 0.25 and 0.33, -76: for higher performance, increase the cut-off and the PME grid spacing. -76: -76: -76: -76: There was 1 NOTE -76: Setting the LD random seed to 1406912477 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to -218142021 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to 2146426873 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -76: Calculating fourier grid dimensions for X Y Z -76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -76: -76: Estimate for the relative computational load of the PME mesh part: 1.00 -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to -237551881 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: Calculating fourier grid dimensions for X Y Z -76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -76: -76: Estimate for the relative computational load of the PME mesh part: 1.00 -76: -76: This run will generate roughly 0 Mb of data -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: -76: Dynamic load balancing report: -76: DLB was turned on during the run due to measured imbalance. -76: Average load imbalance: 9.5%. -76: The balanceable part of the MD step is 44%, load imbalance is computed from this. -76: Part of the total run time spent waiting due to load imbalance: 4.1%. -76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -76: -76: -76: NOTE: 49 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.397 0.099 399.8 -76: (ns/day) (hour/ns) -76: Performance: 18.286 1.312 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (117 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: NOTE: 48 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.087 0.022 399.1 -76: (ns/day) (hour/ns) -76: Performance: 83.401 0.288 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (29 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: -76: Dynamic load balancing report: -76: DLB was off during the run due to low measured imbalance. -76: Average load imbalance: 7.0%. -76: The balanceable part of the MD step is 9%, load imbalance is computed from this. -76: Part of the total run time spent waiting due to load imbalance: 0.6%. -76: -76: -76: NOTE: 26 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.050 0.012 398.0 -76: (ns/day) (hour/ns) -76: Performance: 145.864 0.165 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (151 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.064 0.016 397.4 -76: (ns/day) (hour/ns) -76: Performance: 112.275 0.214 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (109 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 10 to 100, rlist from 1 to 1 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: NOTE: 31 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.043 0.011 397.8 -76: (ns/day) (hour/ns) -76: Performance: 168.827 0.142 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (25 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 10 to 100, rlist from 1 to 1 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.047 0.012 397.1 -76: (ns/day) (hour/ns) -76: Performance: 151.722 0.158 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (24 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (459 ms total) -76: -76: [----------] Global test environment tear-down -76: [==========] 16 tests from 2 test suites ran. (629 ms total) -76: [ PASSED ] 10 tests. -76: [ SKIPPED ] 6 tests, listed below: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76/92 Test #76: MdrunMpiTests ............................. Passed 0.64 sec -test 77 - Start 77: MdrunMultiSimTests - -77: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" -77: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -77: Test timeout computed to be: 600 -77: [==========] Running 2 tests from 1 test suite. -77: [----------] Global test environment set-up. -77: [----------] 2 tests from InNvt/MultiSimTerminationTest -77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) -77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 -77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) -77: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) -77: -77: [----------] Global test environment tear-down -77: [==========] 2 tests from 1 test suite ran. (27 ms total) -77: [ PASSED ] 2 tests. -77: -77: YOU HAVE 4 DISABLED TESTS -77: -77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.04 sec -test 78 - Start 78: MdrunMultiSimReplexTests - -78: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" -78: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -78: Test timeout computed to be: 600 -78: [==========] Running 1 test from 1 test suite. -78: [----------] Global test environment set-up. -78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest -78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) -78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) -78: -78: [----------] Global test environment tear-down -78: [==========] 1 test from 1 test suite ran. (34 ms total) -78: [ PASSED ] 1 test. -78: -78: YOU HAVE 4 DISABLED TESTS -78: -78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.05 sec -test 79 - Start 79: MdrunMultiSimReplexEquivalenceTests - -79: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" -79: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -79: Test timeout computed to be: 600 -79: [==========] Running 0 tests from 0 test suites. -79: [==========] 0 tests from 0 test suites ran. (0 ms total) -79: [ PASSED ] 0 tests. -79: -79: YOU HAVE 10 DISABLED TESTS -79: -79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.01 sec -test 80 - Start 80: MdrunMpi1RankPmeTests - -80: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" -80: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -80: Test timeout computed to be: 600 -80: [==========] Running 19 tests from 1 test suite. -80: [----------] Global test environment set-up. -80: [----------] 19 tests from ReproducesEnergies/PmeTest -80: Number of degrees of freedom in T-Coupling group rest is 12.00 -80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: NVE simulation: will use the initial temperature of 1046.791 K for -80: determining the Verlet buffer size -80: -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: The optimal PME mesh load for parallel simulations is below 0.5 -80: and for highly parallel simulations between 0.25 and 0.33, -80: for higher performance, increase the cut-off and the PME grid spacing. -80: -80: -80: -80: There were 2 NOTEs -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: For a correct single-point energy evaluation with nsteps = 0, use -80: continuation = yes to avoid constraining the input coordinates. -80: -80: Number of degrees of freedom in T-Coupling group rest is 13.00 -80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: NVE simulation: will use the initial temperature of 966.268 K for -80: determining the Verlet buffer size -80: -80: -80: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: The optimal PME mesh load for parallel simulations is below 0.5 -80: and for highly parallel simulations between 0.25 and 0.33, -80: for higher performance, increase the cut-off and the PME grid spacing. -80: -80: -80: -80: There were 3 NOTEs -80: Setting the LD random seed to 1072619247 -80: -80: Generated 8 of the 10 non-bonded parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'Methanol' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -80: -80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -80: -80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Calculating fourier grid dimensions for X Y Z -80: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -80: -80: Estimate for the relative computational load of the PME mesh part: 1.00 -80: -80: This run will generate roughly 0 Mb of data -80: Setting the LD random seed to -281022849 -80: -80: Generated 8 of the 10 non-bonded parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'Methanol' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -80: -80: Searching the wall atom type(s) -80: -80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -80: -80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Calculating fourier grid dimensions for X Y Z -80: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 -80: -80: Estimate for the relative computational load of the PME mesh part: 1.00 -80: -80: This run will generate roughly 0 Mb of data -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.026 0.013 199.3 -80: (ns/day) (hour/ns) -80: Performance: 137.402 0.175 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (159 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.022 0.011 199.3 -80: (ns/day) (hour/ns) -80: Performance: 163.031 0.147 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (18 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 0 steps, 0.0 ps. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.003 0.002 193.3 -80: (ns/day) (hour/ns) -80: Performance: 55.872 0.430 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file -80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (542 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.025 0.013 199.3 -80: (ns/day) (hour/ns) -80: Performance: 144.044 0.167 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (17 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [----------] 19 tests from ReproducesEnergies/PmeTest (740 ms total) -80: -80: [----------] Global test environment tear-down -80: [==========] 19 tests from 1 test suite ran. (776 ms total) -80: [ PASSED ] 4 tests. -80: [ SKIPPED ] 15 tests, listed below: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 0.79 sec -test 81 - Start 81: MdrunMpi2RankPmeTests - -81: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" -81: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -81: Test timeout computed to be: 600 -81: [==========] Running 19 tests from 1 test suite. -81: [----------] Global test environment set-up. -81: [----------] 19 tests from ReproducesEnergies/PmeTest -81: Number of degrees of freedom in T-Coupling group rest is 12.00 -81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: NVE simulation: will use the initial temperature of 1046.791 K for -81: determining the Verlet buffer size -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: The optimal PME mesh load for parallel simulations is below 0.5 -81: and for highly parallel simulations between 0.25 and 0.33, -81: for higher performance, increase the cut-off and the PME grid spacing. -81: -81: -81: -81: There were 2 NOTEs -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: For a correct single-point energy evaluation with nsteps = 0, use -81: continuation = yes to avoid constraining the input coordinates. -81: -81: Number of degrees of freedom in T-Coupling group rest is 13.00 -81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: NVE simulation: will use the initial temperature of 966.268 K for -81: determining the Verlet buffer size -81: -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: The optimal PME mesh load for parallel simulations is below 0.5 -81: and for highly parallel simulations between 0.25 and 0.33, -81: for higher performance, increase the cut-off and the PME grid spacing. -81: -81: -81: -81: There were 3 NOTEs -81: Setting the LD random seed to -8393257 -81: -81: Generated 8 of the 10 non-bonded parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'Methanol' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -81: -81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -81: -81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: Calculating fourier grid dimensions for X Y Z -81: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -81: -81: Estimate for the relative computational load of the PME mesh part: 1.00 -81: -81: This run will generate roughly 0 Mb of data -81: Setting the LD random seed to -541132947 -81: -81: Generated 8 of the 10 non-bonded parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'Methanol' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -81: -81: Searching the wall atom type(s) -81: -81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -81: -81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: Calculating fourier grid dimensions for X Y Z -81: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 -81: -81: Estimate for the relative computational load of the PME mesh part: 1.00 -81: -81: This run will generate roughly 0 Mb of data -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 9.7%. -81: The balanceable part of the MD step is 12%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.2%. -81: -81: -81: NOTE: 31 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.052 0.013 398.4 -81: (ns/day) (hour/ns) -81: Performance: 140.224 0.171 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (151 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was turned on during the run due to measured imbalance. -81: Average load imbalance: 16.8%. -81: The balanceable part of the MD step is 13%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 2.1%. -81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -81: -81: -81: NOTE: 30 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.062 0.015 398.4 -81: (ns/day) (hour/ns) -81: Performance: 117.265 0.205 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (153 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 0 steps, 0.0 ps. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.006 0.002 310.5 -81: (ns/day) (hour/ns) -81: Performance: 43.075 0.557 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (497 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.053 0.013 398.1 -81: (ns/day) (hour/ns) -81: Performance: 136.755 0.175 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (102 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.044 0.011 398.0 -81: (ns/day) (hour/ns) -81: Performance: 162.686 0.148 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (17 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 0 steps, 0.0 ps. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.006 0.002 375.7 -81: (ns/day) (hour/ns) -81: Performance: 53.564 0.448 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (381 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 9.5%. -81: The balanceable part of the MD step is 13%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.2%. -81: -81: -81: NOTE: 31 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.054 0.014 387.6 -81: (ns/day) (hour/ns) -81: Performance: 129.702 0.185 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (22 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [----------] 19 tests from ReproducesEnergies/PmeTest (1327 ms total) -81: -81: [----------] Global test environment tear-down -81: [==========] 19 tests from 1 test suite ran. (1360 ms total) -81: [ PASSED ] 7 tests. -81: [ SKIPPED ] 12 tests, listed below: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 1.37 sec -test 82 - Start 82: MdrunCoordinationBasicTests1Rank - -82: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" -82: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -82: Test timeout computed to be: 1920 -82: [==========] Running 1 test from 1 test suite. -82: [----------] Global test environment set-up. -82: [----------] 1 test from BasicPropagators/PeriodicActionsTest -82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (1) -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: There were 3 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.013 0.013 99.6 -82: (ns/day) (hour/ns) -82: Performance: 111.710 0.215 -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (1) -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: There were 3 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.007 0.007 99.4 -82: (ns/day) (hour/ns) -82: Performance: 215.790 0.111 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (4) -82: -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 4. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 4. -82: -82: -82: There were 5 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.009 0.009 99.6 -82: (ns/day) (hour/ns) -82: Performance: 161.412 0.149 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.023 0.023 99.8 -82: (ns/day) (hour/ns) -82: Performance: 63.375 0.379 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.010 0.010 99.7 -82: (ns/day) (hour/ns) -82: Performance: 146.423 0.164 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.011 0.011 99.6 -82: (ns/day) (hour/ns) -82: Performance: 135.750 0.177 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (113 ms) -82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (113 ms total) -82: -82: [----------] Global test environment tear-down -82: [==========] 1 test from 1 test suite ran. (142 ms total) -82: [ PASSED ] 1 test. -82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.15 sec -test 83 - Start 83: MdrunCoordinationBasicTests2Ranks - -83: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" -83: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -83: Test timeout computed to be: 1920 -83: [==========] Running 1 test from 1 test suite. -83: [----------] Global test environment set-up. -83: [----------] 1 test from BasicPropagators/PeriodicActionsTest -83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (1) -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: There were 3 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 2.1%. -83: The balanceable part of the MD step is 52%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 1.1%. -83: -83: -83: NOTE: 46 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.020 0.010 198.7 -83: (ns/day) (hour/ns) -83: Performance: 148.677 0.161 -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (1) -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: There were 3 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 2.7%. -83: The balanceable part of the MD step is 47%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 1.3%. -83: -83: -83: NOTE: 47 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.020 0.010 198.8 -83: (ns/day) (hour/ns) -83: Performance: 148.416 0.162 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (4) -83: -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 4. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 4. -83: -83: -83: There were 5 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.4%. -83: The balanceable part of the MD step is 42%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.6%. -83: -83: -83: NOTE: 46 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.015 0.008 198.9 -83: (ns/day) (hour/ns) -83: Performance: 191.734 0.125 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 3.3%. -83: The balanceable part of the MD step is 46%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 1.5%. -83: -83: -83: NOTE: 48 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.020 0.010 199.1 -83: (ns/day) (hour/ns) -83: Performance: 146.574 0.164 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 3.9%. -83: The balanceable part of the MD step is 41%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 1.6%. -83: -83: -83: NOTE: 47 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.021 0.011 198.7 -83: (ns/day) (hour/ns) -83: Performance: 138.467 0.173 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.8%. -83: The balanceable part of the MD step is 42%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.7%. -83: -83: -83: NOTE: 47 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.020 0.010 198.7 -83: (ns/day) (hour/ns) -83: Performance: 145.441 0.165 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (106 ms) -83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (106 ms total) -83: -83: [----------] Global test environment tear-down -83: [==========] 1 test from 1 test suite ran. (132 ms total) -83: [ PASSED ] 1 test. -83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 0.14 sec -test 84 - Start 84: MdrunCoordinationCouplingTests1Rank - -84: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" -84: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -84: Test timeout computed to be: 1920 -84: [==========] Running 25 tests from 1 test suite. -84: [----------] Global test environment set-up. -84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 156.067 0.154 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.4 -84: (ns/day) (hour/ns) -84: Performance: 269.622 0.089 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 234.832 0.102 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 165.141 0.145 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.6 -84: (ns/day) (hour/ns) -84: Performance: 126.156 0.190 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.7 -84: (ns/day) (hour/ns) -84: Performance: 137.572 0.174 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (85 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.3 -84: (ns/day) (hour/ns) -84: Performance: 150.755 0.159 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 219.896 0.109 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.6 -84: (ns/day) (hour/ns) -84: Performance: 136.019 0.176 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.5 -84: (ns/day) (hour/ns) -84: Performance: 148.951 0.161 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.6 -84: (ns/day) (hour/ns) -84: Performance: 136.523 0.176 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 179.651 0.134 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (91 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.7 -84: (ns/day) (hour/ns) -84: Performance: 144.456 0.166 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 200.821 0.120 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 191.418 0.125 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.5 -84: (ns/day) (hour/ns) -84: Performance: 150.368 0.160 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.5 -84: (ns/day) (hour/ns) -84: Performance: 164.546 0.146 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 194.986 0.123 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (85 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.7 -84: (ns/day) (hour/ns) -84: Performance: 109.378 0.219 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 245.853 0.098 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 98.9 -84: (ns/day) (hour/ns) -84: Performance: 280.231 0.086 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.4 -84: (ns/day) (hour/ns) -84: Performance: 196.629 0.122 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 157.911 0.152 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.010 99.5 -84: (ns/day) (hour/ns) -84: Performance: 154.127 0.156 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (76 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.5 -84: (ns/day) (hour/ns) -84: Performance: 164.612 0.146 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.7 -84: (ns/day) (hour/ns) -84: Performance: 128.539 0.187 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.7 -84: (ns/day) (hour/ns) -84: Performance: 138.780 0.173 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.7 -84: (ns/day) (hour/ns) -84: Performance: 128.737 0.186 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.8 -84: (ns/day) (hour/ns) -84: Performance: 116.808 0.205 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.038 0.038 99.9 -84: (ns/day) (hour/ns) -84: Performance: 38.551 0.623 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (133 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.032 0.032 99.8 -84: (ns/day) (hour/ns) -84: Performance: 46.011 0.522 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.036 0.036 99.9 -84: (ns/day) (hour/ns) -84: Performance: 40.276 0.596 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 184.361 0.130 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.039 0.039 99.9 -84: (ns/day) (hour/ns) -84: Performance: 38.073 0.630 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.8 -84: (ns/day) (hour/ns) -84: Performance: 93.900 0.256 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.3 -84: (ns/day) (hour/ns) -84: Performance: 217.604 0.110 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (170 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.6 -84: (ns/day) (hour/ns) -84: Performance: 127.739 0.188 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.8 -84: (ns/day) (hour/ns) -84: Performance: 108.800 0.221 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.8 -84: (ns/day) (hour/ns) -84: Performance: 70.473 0.341 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.5 -84: (ns/day) (hour/ns) -84: Performance: 148.552 0.162 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.6 -84: (ns/day) (hour/ns) -84: Performance: 143.842 0.167 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.5 -84: (ns/day) (hour/ns) -84: Performance: 152.671 0.157 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (111 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.5 -84: (ns/day) (hour/ns) -84: Performance: 207.910 0.115 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.4 -84: (ns/day) (hour/ns) -84: Performance: 212.346 0.113 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.3 -84: (ns/day) (hour/ns) -84: Performance: 309.438 0.078 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.4 -84: (ns/day) (hour/ns) -84: Performance: 191.335 0.125 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 248.041 0.097 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.4 -84: (ns/day) (hour/ns) -84: Performance: 186.713 0.129 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (72 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.3 -84: (ns/day) (hour/ns) -84: Performance: 222.332 0.108 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.1 -84: (ns/day) (hour/ns) -84: Performance: 336.902 0.071 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 98.9 -84: (ns/day) (hour/ns) -84: Performance: 304.182 0.079 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.7 -84: (ns/day) (hour/ns) -84: Performance: 116.939 0.205 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.1 -84: (ns/day) (hour/ns) -84: Performance: 243.434 0.099 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.3 -84: (ns/day) (hour/ns) -84: Performance: 229.907 0.104 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (69 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.3 -84: (ns/day) (hour/ns) -84: Performance: 233.153 0.103 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 240.011 0.100 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.3 -84: (ns/day) (hour/ns) -84: Performance: 350.931 0.068 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.3 -84: (ns/day) (hour/ns) -84: Performance: 211.392 0.114 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 270.403 0.089 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 228.229 0.105 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (61 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 264.687 0.091 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 282.156 0.085 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.4 -84: (ns/day) (hour/ns) -84: Performance: 309.873 0.077 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.4 -84: (ns/day) (hour/ns) -84: Performance: 271.583 0.088 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 216.078 0.111 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 255.637 0.094 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (56 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 234.493 0.102 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 283.350 0.085 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 339.128 0.071 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 262.309 0.091 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.1 -84: (ns/day) (hour/ns) -84: Performance: 270.795 0.089 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 240.808 0.100 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (56 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 223.169 0.108 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.5 -84: (ns/day) (hour/ns) -84: Performance: 366.615 0.065 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.5 -84: (ns/day) (hour/ns) -84: Performance: 378.531 0.063 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 253.220 0.095 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 246.050 0.098 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.3 -84: (ns/day) (hour/ns) -84: Performance: 185.181 0.130 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (57 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.7 -84: (ns/day) (hour/ns) -84: Performance: 205.971 0.117 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 369.784 0.065 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 309.065 0.078 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 232.554 0.103 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.6 -84: (ns/day) (hour/ns) -84: Performance: 272.810 0.088 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 258.544 0.093 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (56 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 238.903 0.100 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 313.580 0.077 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 361.962 0.066 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 220.921 0.109 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 242.553 0.099 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 220.723 0.109 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (57 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 229.436 0.105 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 382.812 0.063 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 335.819 0.071 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 255.118 0.094 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 250.065 0.096 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 162.087 0.148 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (59 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.7 -84: (ns/day) (hour/ns) -84: Performance: 243.550 0.099 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.7 -84: (ns/day) (hour/ns) -84: Performance: 312.213 0.077 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.6 -84: (ns/day) (hour/ns) -84: Performance: 358.299 0.067 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.8 -84: (ns/day) (hour/ns) -84: Performance: 173.871 0.138 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.8 -84: (ns/day) (hour/ns) -84: Performance: 218.895 0.110 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.8 -84: (ns/day) (hour/ns) -84: Performance: 195.910 0.123 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (60 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.8 -84: (ns/day) (hour/ns) -84: Performance: 190.371 0.126 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.8 -84: (ns/day) (hour/ns) -84: Performance: 153.313 0.157 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.7 -84: (ns/day) (hour/ns) -84: Performance: 272.195 0.088 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.8 -84: (ns/day) (hour/ns) -84: Performance: 161.133 0.149 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.8 -84: (ns/day) (hour/ns) -84: Performance: 143.916 0.167 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.7 -84: (ns/day) (hour/ns) -84: Performance: 211.632 0.113 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (72 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.8 -84: (ns/day) (hour/ns) -84: Performance: 172.440 0.139 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.7 -84: (ns/day) (hour/ns) -84: Performance: 269.386 0.089 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.8 -84: (ns/day) (hour/ns) -84: Performance: 224.160 0.107 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.8 -84: (ns/day) (hour/ns) -84: Performance: 185.019 0.130 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.8 -84: (ns/day) (hour/ns) -84: Performance: 191.228 0.126 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.8 -84: (ns/day) (hour/ns) -84: Performance: 191.109 0.126 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (67 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 180.129 0.133 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.3 -84: (ns/day) (hour/ns) -84: Performance: 301.001 0.080 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 378.485 0.063 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 195.519 0.123 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 180.440 0.133 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.7 -84: (ns/day) (hour/ns) -84: Performance: 219.254 0.109 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (63 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.8 -84: (ns/day) (hour/ns) -84: Performance: 68.989 0.348 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.8 -84: (ns/day) (hour/ns) -84: Performance: 108.894 0.220 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 241.138 0.100 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 195.030 0.123 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.8 -84: (ns/day) (hour/ns) -84: Performance: 153.043 0.157 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 179.092 0.134 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (91 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.6 -84: (ns/day) (hour/ns) -84: Performance: 127.784 0.188 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 219.919 0.109 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 265.795 0.090 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 167.562 0.143 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 191.495 0.125 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 191.198 0.126 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (72 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.5 -84: (ns/day) (hour/ns) -84: Performance: 202.698 0.118 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.7 -84: (ns/day) (hour/ns) -84: Performance: 224.971 0.107 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 245.110 0.098 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 181.648 0.132 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 169.802 0.141 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 198.045 0.121 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (67 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.4 -84: (ns/day) (hour/ns) -84: Performance: 167.276 0.143 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.5 -84: (ns/day) (hour/ns) -84: Performance: 221.828 0.108 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.5 -84: (ns/day) (hour/ns) -84: Performance: 243.319 0.099 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.4 -84: (ns/day) (hour/ns) -84: Performance: 169.410 0.142 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 180.424 0.133 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 192.814 0.124 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (72 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.012 99.7 -84: (ns/day) (hour/ns) -84: Performance: 127.604 0.188 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.006 0.006 99.6 -84: (ns/day) (hour/ns) -84: Performance: 251.597 0.095 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.6 -84: (ns/day) (hour/ns) -84: Performance: 269.245 0.089 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.7 -84: (ns/day) (hour/ns) -84: Performance: 183.937 0.130 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.5 -84: (ns/day) (hour/ns) -84: Performance: 194.611 0.123 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 219.176 0.110 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (69 ms) -84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1942 ms total) -84: -84: [----------] Global test environment tear-down -84: [==========] 25 tests from 1 test suite ran. (1966 ms total) -84: [ PASSED ] 25 tests. -84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 1.98 sec -test 85 - Start 85: MdrunCoordinationCouplingTests2Ranks - -85: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" -85: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -85: Test timeout computed to be: 1920 -85: [==========] Running 25 tests from 1 test suite. -85: [----------] Global test environment set-up. -85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.7%. -85: The balanceable part of the MD step is 48%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.3%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 141.305 0.170 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.4%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.5%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 197.9 -85: (ns/day) (hour/ns) -85: Performance: 263.826 0.091 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.8%. -85: The balanceable part of the MD step is 36%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.009 0.005 198.2 -85: (ns/day) (hour/ns) -85: Performance: 325.080 0.074 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.9%. -85: The balanceable part of the MD step is 37%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.5%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.005 198.5 -85: (ns/day) (hour/ns) -85: Performance: 269.581 0.089 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.2%. -85: The balanceable part of the MD step is 34%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.1%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 211.294 0.114 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.5%. -85: The balanceable part of the MD step is 39%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.6%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 199.1 -85: (ns/day) (hour/ns) -85: Performance: 175.316 0.137 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (71 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.7%. -85: The balanceable part of the MD step is 54%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.9%. -85: -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.6 -85: (ns/day) (hour/ns) -85: Performance: 245.354 0.098 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.8%. -85: The balanceable part of the MD step is 49%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.3%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.010 0.005 198.3 -85: (ns/day) (hour/ns) -85: Performance: 301.849 0.080 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.8%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.2%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.010 0.005 197.9 -85: (ns/day) (hour/ns) -85: Performance: 280.167 0.086 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 5.0%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.2%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 181.082 0.133 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.1%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 221.887 0.108 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.4%. -85: The balanceable part of the MD step is 42%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 192.305 0.125 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (64 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.3%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 214.259 0.112 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.5%. -85: The balanceable part of the MD step is 50%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.3%. -85: -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.010 0.005 198.4 -85: (ns/day) (hour/ns) -85: Performance: 279.272 0.086 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.4%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.8%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 205.624 0.117 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 4.0%. -85: The balanceable part of the MD step is 41%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 199.0 -85: (ns/day) (hour/ns) -85: Performance: 167.665 0.143 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.5%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 214.793 0.112 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.5%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.1%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 204.054 0.118 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (68 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.2%. -85: The balanceable part of the MD step is 54%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.2%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 147.008 0.163 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.7%. -85: The balanceable part of the MD step is 48%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.3%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 198.6 -85: (ns/day) (hour/ns) -85: Performance: 256.211 0.094 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.0%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.4%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 211.712 0.113 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.2%. -85: The balanceable part of the MD step is 45%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 188.299 0.127 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.6%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.9%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 187.566 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.3%. -85: The balanceable part of the MD step is 42%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 199.0 -85: (ns/day) (hour/ns) -85: Performance: 169.608 0.142 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (73 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 190.866 0.126 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.034 0.017 199.6 -85: (ns/day) (hour/ns) -85: Performance: 86.219 0.278 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 235.736 0.102 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.026 0.013 199.4 -85: (ns/day) (hour/ns) -85: Performance: 113.382 0.212 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.6 -85: (ns/day) (hour/ns) -85: Performance: 187.920 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 181.782 0.132 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (86 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 174.890 0.137 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 198.4 -85: (ns/day) (hour/ns) -85: Performance: 257.954 0.093 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.4 -85: (ns/day) (hour/ns) -85: Performance: 241.044 0.100 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.6 -85: (ns/day) (hour/ns) -85: Performance: 223.961 0.107 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 190.648 0.126 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.025 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 118.480 0.203 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (74 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 200.152 0.120 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 209.555 0.115 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.5 -85: (ns/day) (hour/ns) -85: Performance: 238.593 0.101 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.6 -85: (ns/day) (hour/ns) -85: Performance: 218.364 0.110 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.4 -85: (ns/day) (hour/ns) -85: Performance: 237.210 0.101 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 200.834 0.120 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (67 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 209.576 0.115 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 198.3 -85: (ns/day) (hour/ns) -85: Performance: 262.304 0.091 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.005 198.4 -85: (ns/day) (hour/ns) -85: Performance: 276.056 0.087 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 175.581 0.137 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 177.242 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.6 -85: (ns/day) (hour/ns) -85: Performance: 209.940 0.114 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (67 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 203.484 0.118 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 218.938 0.110 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 241.450 0.099 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 215.131 0.112 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 199.2 -85: (ns/day) (hour/ns) -85: Performance: 155.706 0.154 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 194.617 0.123 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (71 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 124.966 0.192 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.010 0.005 198.5 -85: (ns/day) (hour/ns) -85: Performance: 281.357 0.085 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 197.8 -85: (ns/day) (hour/ns) -85: Performance: 259.426 0.093 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 207.267 0.116 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 193.812 0.124 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 179.969 0.133 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (74 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.4 -85: (ns/day) (hour/ns) -85: Performance: 163.028 0.147 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.5 -85: (ns/day) (hour/ns) -85: Performance: 240.193 0.100 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 196.9 -85: (ns/day) (hour/ns) -85: Performance: 258.295 0.093 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 186.920 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 187.975 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 199.0 -85: (ns/day) (hour/ns) -85: Performance: 166.193 0.144 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (75 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.3 -85: (ns/day) (hour/ns) -85: Performance: 183.057 0.131 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 191.811 0.125 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.006 198.5 -85: (ns/day) (hour/ns) -85: Performance: 228.043 0.105 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.6 -85: (ns/day) (hour/ns) -85: Performance: 198.889 0.121 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.0 -85: (ns/day) (hour/ns) -85: Performance: 148.282 0.162 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 180.885 0.133 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (81 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.4 -85: (ns/day) (hour/ns) -85: Performance: 182.701 0.131 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 223.081 0.108 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.1 -85: (ns/day) (hour/ns) -85: Performance: 217.355 0.110 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 199.3 -85: (ns/day) (hour/ns) -85: Performance: 140.870 0.170 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.8 -85: (ns/day) (hour/ns) -85: Performance: 153.121 0.157 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 199.3 -85: (ns/day) (hour/ns) -85: Performance: 140.222 0.171 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (91 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.040 0.020 199.6 -85: (ns/day) (hour/ns) -85: Performance: 72.941 0.329 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 213.232 0.113 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 262.214 0.092 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.2 -85: (ns/day) (hour/ns) -85: Performance: 148.870 0.161 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 181.242 0.132 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 199.0 -85: (ns/day) (hour/ns) -85: Performance: 151.530 0.158 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (98 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 199.2 -85: (ns/day) (hour/ns) -85: Performance: 157.530 0.152 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.8 -85: (ns/day) (hour/ns) -85: Performance: 237.994 0.101 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 216.104 0.111 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 126.952 0.189 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.028 0.014 199.4 -85: (ns/day) (hour/ns) -85: Performance: 105.889 0.227 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 199.2 -85: (ns/day) (hour/ns) -85: Performance: 158.086 0.152 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (92 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 176.914 0.136 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 151.052 0.159 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 201.914 0.119 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 143.256 0.168 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 193.943 0.124 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 184.394 0.130 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (79 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.2%. -85: The balanceable part of the MD step is 60%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.5 -85: (ns/day) (hour/ns) -85: Performance: 136.697 0.176 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.4%. -85: The balanceable part of the MD step is 58%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.0%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 177.475 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.1%. -85: The balanceable part of the MD step is 50%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.5 -85: (ns/day) (hour/ns) -85: Performance: 185.075 0.130 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.1%. -85: The balanceable part of the MD step is 50%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.2 -85: (ns/day) (hour/ns) -85: Performance: 125.699 0.191 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.0%. -85: The balanceable part of the MD step is 42%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.5%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.028 0.014 198.5 -85: (ns/day) (hour/ns) -85: Performance: 105.099 0.228 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.4%. -85: The balanceable part of the MD step is 48%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.032 0.016 198.9 -85: (ns/day) (hour/ns) -85: Performance: 92.098 0.261 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (94 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.1%. -85: The balanceable part of the MD step is 60%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.2%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.025 0.013 198.8 -85: (ns/day) (hour/ns) -85: Performance: 115.621 0.208 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.1%. -85: The balanceable part of the MD step is 56%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.7%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 167.793 0.143 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.4%. -85: The balanceable part of the MD step is 56%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 171.485 0.140 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.5%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.2 -85: (ns/day) (hour/ns) -85: Performance: 122.017 0.197 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.3%. -85: The balanceable part of the MD step is 53%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.2%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.030 0.015 198.9 -85: (ns/day) (hour/ns) -85: Performance: 96.621 0.248 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.2%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.027 0.014 198.7 -85: (ns/day) (hour/ns) -85: Performance: 108.522 0.221 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (97 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.5%. -85: The balanceable part of the MD step is 33%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.6 -85: (ns/day) (hour/ns) -85: Performance: 132.801 0.181 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.6%. -85: The balanceable part of the MD step is 34%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 170.933 0.140 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.2%. -85: The balanceable part of the MD step is 55%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.027 0.014 198.7 -85: (ns/day) (hour/ns) -85: Performance: 108.314 0.222 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.9%. -85: The balanceable part of the MD step is 54%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.6%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 198.4 -85: (ns/day) (hour/ns) -85: Performance: 140.952 0.170 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.9%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.0 -85: (ns/day) (hour/ns) -85: Performance: 142.600 0.168 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.8%. -85: The balanceable part of the MD step is 50%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.4%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.4 -85: (ns/day) (hour/ns) -85: Performance: 142.418 0.169 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (96 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.2 -85: (ns/day) (hour/ns) -85: Performance: 170.507 0.141 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 197.6 -85: (ns/day) (hour/ns) -85: Performance: 208.068 0.115 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.8 -85: (ns/day) (hour/ns) -85: Performance: 177.610 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 136.506 0.176 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.2 -85: (ns/day) (hour/ns) -85: Performance: 130.058 0.185 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 198.2 -85: (ns/day) (hour/ns) -85: Performance: 157.236 0.153 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (85 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.025 0.012 198.7 -85: (ns/day) (hour/ns) -85: Performance: 118.416 0.203 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 167.706 0.143 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.029 0.015 198.8 -85: (ns/day) (hour/ns) -85: Performance: 99.946 0.240 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.5 -85: (ns/day) (hour/ns) -85: Performance: 124.287 0.193 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.1 -85: (ns/day) (hour/ns) -85: Performance: 129.863 0.185 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.4 -85: (ns/day) (hour/ns) -85: Performance: 136.499 0.176 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (107 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.6 -85: (ns/day) (hour/ns) -85: Performance: 129.970 0.185 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 132.961 0.181 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 196.4 -85: (ns/day) (hour/ns) -85: Performance: 231.915 0.103 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 155.872 0.154 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.026 0.013 198.6 -85: (ns/day) (hour/ns) -85: Performance: 112.311 0.214 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.4 -85: (ns/day) (hour/ns) -85: Performance: 134.118 0.179 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (112 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.5 -85: (ns/day) (hour/ns) -85: Performance: 149.896 0.160 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 167.303 0.143 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 146.740 0.164 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 157.481 0.152 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.011 198.4 -85: (ns/day) (hour/ns) -85: Performance: 128.002 0.187 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 172.226 0.139 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (90 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 159.473 0.150 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 133.479 0.180 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 159.057 0.151 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.029 0.014 198.7 -85: (ns/day) (hour/ns) -85: Performance: 101.583 0.236 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.4 -85: (ns/day) (hour/ns) -85: Performance: 127.415 0.188 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 134.050 0.179 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (98 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.7 -85: (ns/day) (hour/ns) -85: Performance: 122.990 0.195 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.4 -85: (ns/day) (hour/ns) -85: Performance: 130.388 0.184 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 198.4 -85: (ns/day) (hour/ns) -85: Performance: 141.930 0.169 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.5 -85: (ns/day) (hour/ns) -85: Performance: 125.953 0.191 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.029 0.015 198.8 -85: (ns/day) (hour/ns) -85: Performance: 100.778 0.238 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.064 0.032 199.4 -85: (ns/day) (hour/ns) -85: Performance: 45.937 0.522 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (122 ms) -85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (2146 ms total) -85: -85: [----------] Global test environment tear-down -85: [==========] 25 tests from 1 test suite ran. (2166 ms total) -85: [ PASSED ] 25 tests. -85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 2.18 sec -test 86 - Start 86: MdrunCoordinationConstraintsTests1Rank - -86: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" -86: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -86: Test timeout computed to be: 1920 -86: [==========] Running 13 tests from 1 test suite. -86: [----------] Global test environment set-up. -86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.046 0.046 99.9 -86: (ns/day) (hour/ns) -86: Performance: 31.876 0.753 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 98.6 -86: (ns/day) (hour/ns) -86: Performance: 344.263 0.070 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 98.8 -86: (ns/day) (hour/ns) -86: Performance: 337.530 0.071 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 209.032 0.115 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.3 -86: (ns/day) (hour/ns) -86: Performance: 135.914 0.177 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 219.645 0.109 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1308 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 173.930 0.138 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.2 -86: (ns/day) (hour/ns) -86: Performance: 282.648 0.085 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.006 99.0 -86: (ns/day) (hour/ns) -86: Performance: 266.646 0.090 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.0 -86: (ns/day) (hour/ns) -86: Performance: 249.599 0.096 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.1 -86: (ns/day) (hour/ns) -86: Performance: 208.565 0.115 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 220.944 0.109 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1268 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.2 -86: (ns/day) (hour/ns) -86: Performance: 164.651 0.146 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 203.394 0.118 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.0 -86: (ns/day) (hour/ns) -86: Performance: 275.272 0.087 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.3 -86: (ns/day) (hour/ns) -86: Performance: 148.634 0.161 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.1 -86: (ns/day) (hour/ns) -86: Performance: 237.971 0.101 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 180.393 0.133 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1263 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.1 -86: (ns/day) (hour/ns) -86: Performance: 248.842 0.096 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.0 -86: (ns/day) (hour/ns) -86: Performance: 288.161 0.083 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.0 -86: (ns/day) (hour/ns) -86: Performance: 280.550 0.086 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.013 0.013 99.6 -86: (ns/day) (hour/ns) -86: Performance: 110.085 0.218 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 163.420 0.147 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 223.331 0.107 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1263 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.2 -86: (ns/day) (hour/ns) -86: Performance: 193.286 0.124 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 98.9 -86: (ns/day) (hour/ns) -86: Performance: 288.161 0.083 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.2 -86: (ns/day) (hour/ns) -86: Performance: 291.874 0.082 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 217.827 0.110 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.0 -86: (ns/day) (hour/ns) -86: Performance: 215.654 0.111 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 193.346 0.124 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1261 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 191.448 0.125 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.0 -86: (ns/day) (hour/ns) -86: Performance: 271.763 0.088 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 211.988 0.113 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.0 -86: (ns/day) (hour/ns) -86: Performance: 199.974 0.120 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 215.022 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 182.986 0.131 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1247 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.177 0.177 100.0 -86: (ns/day) (hour/ns) -86: Performance: 8.286 2.896 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.023 0.023 99.8 -86: (ns/day) (hour/ns) -86: Performance: 64.290 0.373 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.175 0.175 100.0 -86: (ns/day) (hour/ns) -86: Performance: 8.382 2.863 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 175.002 0.137 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 201.432 0.119 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 210.972 0.114 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1678 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.013 0.013 99.5 -86: (ns/day) (hour/ns) -86: Performance: 111.323 0.216 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 222.863 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.0 -86: (ns/day) (hour/ns) -86: Performance: 248.311 0.097 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.1 -86: (ns/day) (hour/ns) -86: Performance: 214.737 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 199.656 0.120 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 232.090 0.103 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1270 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 181.895 0.132 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 98.9 -86: (ns/day) (hour/ns) -86: Performance: 258.360 0.093 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 260.182 0.092 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.014 0.014 99.8 -86: (ns/day) (hour/ns) -86: Performance: 107.712 0.223 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.2 -86: (ns/day) (hour/ns) -86: Performance: 169.905 0.141 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 160.036 0.150 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1271 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 154.890 0.155 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 174.818 0.137 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.7 -86: (ns/day) (hour/ns) -86: Performance: 186.459 0.129 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 143.577 0.167 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 162.677 0.148 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 160.303 0.150 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1279 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 157.302 0.153 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 177.100 0.136 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 164.969 0.145 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.6 -86: (ns/day) (hour/ns) -86: Performance: 137.667 0.174 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.5 -86: (ns/day) (hour/ns) -86: Performance: 149.409 0.161 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 173.626 0.138 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1637 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.014 0.014 99.6 -86: (ns/day) (hour/ns) -86: Performance: 107.993 0.222 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 209.758 0.114 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 197.392 0.122 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.010 99.6 -86: (ns/day) (hour/ns) -86: Performance: 154.165 0.156 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 157.733 0.152 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 184.239 0.130 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1278 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.6 -86: (ns/day) (hour/ns) -86: Performance: 157.030 0.153 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 211.479 0.113 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 214.602 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.121 0.121 99.9 -86: (ns/day) (hour/ns) -86: Performance: 12.134 1.978 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.4 -86: (ns/day) (hour/ns) -86: Performance: 183.307 0.131 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 175.226 0.137 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1382 ms) -86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (17411 ms total) -86: -86: [----------] Global test environment tear-down -86: [==========] 13 tests from 1 test suite ran. (17433 ms total) -86: [ PASSED ] 13 tests. -86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 17.45 sec -test 87 - Start 87: MdrunCoordinationConstraintsTests2Ranks - -87: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" -87: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -87: Test timeout computed to be: 1920 -87: [==========] Running 13 tests from 1 test suite. -87: [----------] Global test environment set-up. -87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB got disabled because it was unsuitable to use. -87: Average load imbalance: 4.1%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.1%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.3 -87: (ns/day) (hour/ns) -87: Performance: 161.710 0.148 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.9%. -87: The balanceable part of the MD step is 45%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.005 198.3 -87: (ns/day) (hour/ns) -87: Performance: 267.765 0.090 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.5%. -87: The balanceable part of the MD step is 34%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 42 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 196.7 -87: (ns/day) (hour/ns) -87: Performance: 304.731 0.079 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.8%. -87: The balanceable part of the MD step is 38%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.8%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 221.218 0.108 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.8%. -87: The balanceable part of the MD step is 37%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.9 -87: (ns/day) (hour/ns) -87: Performance: 210.932 0.114 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.0%. -87: The balanceable part of the MD step is 35%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.5 -87: (ns/day) (hour/ns) -87: Performance: 233.958 0.103 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1327 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 53%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 43 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 197.5 -87: (ns/day) (hour/ns) -87: Performance: 223.400 0.107 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB got disabled because it was unsuitable to use. -87: Average load imbalance: 9.5%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 4.5%. -87: -87: -87: NOTE: 42 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 196.8 -87: (ns/day) (hour/ns) -87: Performance: 283.500 0.085 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 42%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 198.4 -87: (ns/day) (hour/ns) -87: Performance: 232.537 0.103 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 40%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.5 -87: (ns/day) (hour/ns) -87: Performance: 225.522 0.106 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 216.085 0.111 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.6%. -87: The balanceable part of the MD step is 42%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.9%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 199.0 -87: (ns/day) (hour/ns) -87: Performance: 146.358 0.164 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1312 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.5%. -87: The balanceable part of the MD step is 52%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 199.3 -87: (ns/day) (hour/ns) -87: Performance: 87.391 0.275 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.031 0.015 199.3 -87: (ns/day) (hour/ns) -87: Performance: 95.719 0.251 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.9%. -87: The balanceable part of the MD step is 39%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.3%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 198.9 -87: (ns/day) (hour/ns) -87: Performance: 87.172 0.275 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.2%. -87: The balanceable part of the MD step is 40%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.062 0.031 199.5 -87: (ns/day) (hour/ns) -87: Performance: 46.922 0.511 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.9%. -87: The balanceable part of the MD step is 39%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.3%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.035 0.018 198.9 -87: (ns/day) (hour/ns) -87: Performance: 83.038 0.289 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB got disabled because it was unsuitable to use. -87: Average load imbalance: 5.7%. -87: The balanceable part of the MD step is 38%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.2%. -87: -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.046 0.023 199.0 -87: (ns/day) (hour/ns) -87: Performance: 64.215 0.374 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1396 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.6 -87: (ns/day) (hour/ns) -87: Performance: 195.711 0.123 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 197.3 -87: (ns/day) (hour/ns) -87: Performance: 261.580 0.092 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 196.4 -87: (ns/day) (hour/ns) -87: Performance: 291.557 0.082 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 197.1 -87: (ns/day) (hour/ns) -87: Performance: 230.989 0.104 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.0 -87: (ns/day) (hour/ns) -87: Performance: 233.692 0.103 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.7 -87: (ns/day) (hour/ns) -87: Performance: 204.664 0.117 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1313 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.2 -87: (ns/day) (hour/ns) -87: Performance: 211.171 0.114 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 197.3 -87: (ns/day) (hour/ns) -87: Performance: 252.685 0.095 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 198.0 -87: (ns/day) (hour/ns) -87: Performance: 264.955 0.091 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 197.3 -87: (ns/day) (hour/ns) -87: Performance: 229.133 0.105 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 215.613 0.111 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 216.321 0.111 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1315 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 197.3 -87: (ns/day) (hour/ns) -87: Performance: 194.497 0.123 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.1 -87: (ns/day) (hour/ns) -87: Performance: 294.364 0.082 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.005 198.2 -87: (ns/day) (hour/ns) -87: Performance: 276.396 0.087 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 197.8 -87: (ns/day) (hour/ns) -87: Performance: 197.354 0.122 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.2 -87: (ns/day) (hour/ns) -87: Performance: 181.301 0.132 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.6 -87: (ns/day) (hour/ns) -87: Performance: 201.914 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1309 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.1 -87: (ns/day) (hour/ns) -87: Performance: 200.335 0.120 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.0 -87: (ns/day) (hour/ns) -87: Performance: 286.453 0.084 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.4 -87: (ns/day) (hour/ns) -87: Performance: 162.277 0.148 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.9 -87: (ns/day) (hour/ns) -87: Performance: 214.393 0.112 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.5 -87: (ns/day) (hour/ns) -87: Performance: 202.985 0.118 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.2 -87: (ns/day) (hour/ns) -87: Performance: 187.099 0.128 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1320 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.1 -87: (ns/day) (hour/ns) -87: Performance: 182.623 0.131 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.9 -87: (ns/day) (hour/ns) -87: Performance: 244.779 0.098 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.5 -87: (ns/day) (hour/ns) -87: Performance: 279.963 0.086 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.1 -87: (ns/day) (hour/ns) -87: Performance: 212.812 0.113 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.5 -87: (ns/day) (hour/ns) -87: Performance: 157.925 0.152 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.046 0.023 199.5 -87: (ns/day) (hour/ns) -87: Performance: 63.648 0.377 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1324 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.031 0.016 198.7 -87: (ns/day) (hour/ns) -87: Performance: 93.838 0.256 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.1 -87: (ns/day) (hour/ns) -87: Performance: 209.580 0.115 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.9 -87: (ns/day) (hour/ns) -87: Performance: 242.658 0.099 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.3 -87: (ns/day) (hour/ns) -87: Performance: 188.354 0.127 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.355 0.178 199.9 -87: (ns/day) (hour/ns) -87: Performance: 8.268 2.903 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 203.059 0.118 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1493 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.2%. -87: The balanceable part of the MD step is 55%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.2%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.8 -87: (ns/day) (hour/ns) -87: Performance: 157.100 0.153 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.2%. -87: The balanceable part of the MD step is 56%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 196.6 -87: (ns/day) (hour/ns) -87: Performance: 188.883 0.127 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.1%. -87: The balanceable part of the MD step is 48%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.085 0.042 199.4 -87: (ns/day) (hour/ns) -87: Performance: 34.637 0.693 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.6%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.3%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.026 0.013 197.7 -87: (ns/day) (hour/ns) -87: Performance: 110.661 0.217 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.0%. -87: The balanceable part of the MD step is 46%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.9%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.1 -87: (ns/day) (hour/ns) -87: Performance: 161.513 0.149 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.9%. -87: The balanceable part of the MD step is 46%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 197.8 -87: (ns/day) (hour/ns) -87: Performance: 139.112 0.173 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1368 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.3%. -87: The balanceable part of the MD step is 57%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.2%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 197.5 -87: (ns/day) (hour/ns) -87: Performance: 142.826 0.168 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.7%. -87: The balanceable part of the MD step is 56%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.0%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 196.3 -87: (ns/day) (hour/ns) -87: Performance: 208.975 0.115 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.6%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.3%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 196.4 -87: (ns/day) (hour/ns) -87: Performance: 201.560 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.7%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.3%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 197.2 -87: (ns/day) (hour/ns) -87: Performance: 146.312 0.164 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.1%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.010 197.0 -87: (ns/day) (hour/ns) -87: Performance: 153.629 0.156 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.2%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.010 197.2 -87: (ns/day) (hour/ns) -87: Performance: 153.277 0.157 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1323 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.2 -87: (ns/day) (hour/ns) -87: Performance: 159.744 0.150 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 196.0 -87: (ns/day) (hour/ns) -87: Performance: 187.946 0.128 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 196.2 -87: (ns/day) (hour/ns) -87: Performance: 185.401 0.129 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 196.8 -87: (ns/day) (hour/ns) -87: Performance: 157.070 0.153 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.009 197.0 -87: (ns/day) (hour/ns) -87: Performance: 155.349 0.154 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 196.7 -87: (ns/day) (hour/ns) -87: Performance: 143.325 0.167 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1337 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.056 0.028 198.5 -87: (ns/day) (hour/ns) -87: Performance: 52.330 0.459 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 196.8 -87: (ns/day) (hour/ns) -87: Performance: 136.185 0.176 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 196.0 -87: (ns/day) (hour/ns) -87: Performance: 197.107 0.122 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 196.1 -87: (ns/day) (hour/ns) -87: Performance: 176.524 0.136 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.027 0.014 197.2 -87: (ns/day) (hour/ns) -87: Performance: 107.903 0.222 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.064 0.032 198.9 -87: (ns/day) (hour/ns) -87: Performance: 45.683 0.525 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1370 ms) -87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (17513 ms total) -87: -87: [----------] Global test environment tear-down -87: [==========] 13 tests from 1 test suite ran. (17543 ms total) -87: [ PASSED ] 13 tests. -87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 17.56 sec -test 88 - Start 88: MdrunFEPTests - -88: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunFEPTests.xml" -88: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -88: Test timeout computed to be: 600 -88: [==========] Running 14 tests from 2 test suites. -88: [----------] Global test environment set-up. -88: [----------] 2 tests from ExpandedEnsembleTest -88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 79.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 2 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 16 steps, 0.0 ps. -88: Generated 2485 of the 2485 non-bonded parameter combinations -88: -88: Generated 2485 of the 2485 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'nonanol' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.032 0.016 199.4 -88: (ns/day) (hour/ns) -88: Performance: 90.429 0.265 -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps -88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -88: -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.024 0.012 198.4 -88: (ns/day) (hour/ns) -88: Performance: 63.166 0.380 -88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (64 ms) -88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 79.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 2 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 1 steps, 0.0 ps. -88: Generated 2485 of the 2485 non-bonded parameter combinations -88: -88: Generated 2485 of the 2485 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'nonanol' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.024 0.012 199.6 -88: (ns/day) (hour/ns) -88: Performance: 14.163 1.695 -88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (28 ms) -88: [----------] 2 tests from ExpandedEnsembleTest (92 ms total) -88: -88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -279135041 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.066 0.033 199.6 -88: (ns/day) (hour/ns) -88: Performance: 55.178 0.435 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (254 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -12615763 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.077 0.039 199.7 -88: (ns/day) (hour/ns) -88: Performance: 46.869 0.512 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (122 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 4 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -1694633996 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.053 0.027 199.6 -88: (ns/day) (hour/ns) -88: Performance: 68.340 0.351 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (110 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: NOTE 3 [file topol.top, line 155]: -88: System has non-zero total charge: 1.000000 -88: Total charge should normally be an integer. See -88: https://manual.gromacs.org/current/user-guide/floating-point.html -88: for discussion on how close it should be to an integer. -88: -88: -88: -88: -88: WARNING 2 [file topol.top, line 155]: -88: You are using Ewald electrostatics in a system with net charge. This can -88: lead to severe artifacts, such as ions moving into regions with low -88: dielectric, due to the uniform background charge. We suggest to -88: neutralize your system with counter ions, possibly in combination with a -88: physiological salt concentration. -88: -88: Setting the LD random seed to 536067050 -88: -88: Generated 171 of the 171 non-bonded parameter combinations -88: -88: Generated 171 of the 171 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'NA' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -88: Charge -88: J. Chem. Theory Comput. (2014) -88: DOI: 10.1021/ct400626b -88: -------- -------- --- Thank You --- -------- -------- -88: -88: Number of degrees of freedom in T-Coupling group System is 358.00 -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 5 NOTEs -88: -88: There were 2 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: There are: 1 Ion residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.96 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.055 0.028 199.6 -88: (ns/day) (hour/ns) -88: Performance: 65.880 0.364 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (203 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: NOTE 3 [file topol.top, line 165]: -88: System has non-zero total charge: 1.000000 -88: Total charge should normally be an integer. See -88: https://manual.gromacs.org/current/user-guide/floating-point.html -88: for discussion on how close it should be to an integer. -88: -88: -88: -88: -88: WARNING 2 [file topol.top, line 165]: -88: You are using Ewald electrostatics in a system with net charge. This can -88: lead to severe artifacts, such as ions moving into regions with low -88: dielectric, due to the uniform background charge. We suggest to -88: neutralize your system with counter ions, possibly in combination with a -88: physiological salt concentration. -88: -88: Setting the LD random seed to 1693020159 -88: -88: Generated 190 of the 190 non-bonded parameter combinations -88: -88: Generated 190 of the 190 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'NA' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'CL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'CL' -88: -88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -88: Charge -88: J. Chem. Theory Comput. (2014) -88: DOI: 10.1021/ct400626b -88: -------- -------- --- Thank You --- -------- -------- -88: -88: Number of degrees of freedom in T-Coupling group System is 361.00 -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 5 NOTEs -88: -88: There were 2 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: There are: 2 Ion residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.96 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.054 0.027 199.6 -88: (ns/day) (hour/ns) -88: Performance: 66.690 0.360 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (44 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off -88: and vdw_modifier=Force-switch -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 4 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 100 steps, 0.1 ps. -88: Setting the LD random seed to 2046743503 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.240 0.120 199.9 -88: (ns/day) (hour/ns) -88: Performance: 72.717 0.330 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (205 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: WARNING 2 [file topol.top, line 72]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 8 1'. -88: -88: -88: WARNING 3 [file topol.top, line 73]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 9 1'. -88: -88: -88: WARNING 4 [file topol.top, line 98]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '6 5 7 1'. -88: -88: -88: WARNING 5 [file topol.top, line 99]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 8 1'. -88: -88: -88: WARNING 6 [file topol.top, line 100]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 9 1'. -88: -88: -88: WARNING 7 [file topol.top, line 101]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '8 7 9 1'. -88: -88: -88: WARNING 8 [file topol.top, line 111]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 8 3'. -88: -88: -88: WARNING 9 [file topol.top, line 112]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 9 3'. -88: -88: -88: WARNING 10 [file topol.top, line 113]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 8 3'. -88: -88: -88: WARNING 11 [file topol.top, line 114]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 9 3'. -88: -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 2 NOTEs -88: -88: There were 11 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to 1597955915 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.089 0.045 199.7 -88: (ns/day) (hour/ns) -88: Performance: 40.757 0.589 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (129 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: WARNING 2 [file topol.top, line 72]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 8 1'. -88: -88: -88: WARNING 3 [file topol.top, line 73]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 9 1'. -88: -88: -88: WARNING 4 [file topol.top, line 98]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '6 5 7 1'. -88: -88: -88: WARNING 5 [file topol.top, line 99]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 8 1'. -88: -88: -88: WARNING 6 [file topol.top, line 100]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 9 1'. -88: -88: -88: WARNING 7 [file topol.top, line 101]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '8 7 9 1'. -88: -88: -88: WARNING 8 [file topol.top, line 111]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 8 3'. -88: -88: -88: WARNING 9 [file topol.top, line 112]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 9 3'. -88: -88: -88: WARNING 10 [file topol.top, line 113]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 8 3'. -88: -88: -88: WARNING 11 [file topol.top, line 114]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 9 3'. -88: -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: Removing center of mass motion in the presence of position restraints -88: might cause artifacts. When you are using position restraints to -88: equilibrate a macro-molecule, the artifacts are usually negligible. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There were 11 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -287900246 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.087 0.044 199.7 -88: (ns/day) (hour/ns) -88: Performance: 41.578 0.577 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (129 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 2 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to 1559650300 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.88 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.042 0.021 199.2 -88: (ns/day) (hour/ns) -88: Performance: 85.352 0.281 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (102 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: There was 1 NOTE -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.031 0.015 199.0 -88: (ns/day) (hour/ns) -88: Performance: 117.700 0.204 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -8421737 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.88 -88: -88: This run will generate roughly 0 Mb of data -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (96 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -775947485 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.94 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.085 0.043 199.6 -88: (ns/day) (hour/ns) -88: Performance: 42.685 0.562 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (126 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -1073814380 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.88 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.040 0.020 199.3 -88: (ns/day) (hour/ns) -88: Performance: 90.430 0.265 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (100 ms) -88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (1626 ms total) -88: -88: [----------] Global test environment tear-down -88: [==========] 14 tests from 2 test suites ran. (1767 ms total) -88: [ PASSED ] 14 tests. -88/92 Test #88: MdrunFEPTests ............................. Passed 1.78 sec -test 89 - Start 89: MdrunPullTests - -89: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunPullTests.xml" -89: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -89: Test timeout computed to be: 600 -89: [==========] Running 4 tests from 1 test suite. -89: [----------] Global test environment set-up. -89: [----------] 4 tests from PullTest/PullIntegrationTest -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.600 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.040 0.020 199.4 -89: (ns/day) (hour/ns) -89: Performance: 89.669 0.268 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (240 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.301 nm 0.400 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.034 0.017 199.5 -89: (ns/day) (hour/ns) -89: Performance: 106.582 0.225 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (230 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Pull group 3 'r_3' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1292.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.357 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.500 nm -89: 1 3 2 -89: 3 3 8 0.331 nm 0.400 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.032 0.016 199.4 -89: (ns/day) (hour/ns) -89: Performance: 114.212 0.210 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (231 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.000 nm -89: 1 3 2 -89: 2 3 5 0.050 nm 0.000 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.036 0.018 199.2 -89: (ns/day) (hour/ns) -89: Performance: 99.926 0.240 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (234 ms) -89: [----------] 4 tests from PullTest/PullIntegrationTest (937 ms total) -89: -89: [----------] Global test environment tear-down -89: [==========] 4 tests from 1 test suite ran. (962 ms total) -89: [ PASSED ] 4 tests. -89/92 Test #89: MdrunPullTests ............................ Passed 0.98 sec -test 90 - Start 90: MdrunRotationTests - -90: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunRotationTests.xml" -90: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -90: Test timeout computed to be: 600 -90: [==========] Running 12 tests from 1 test suite. -90: [----------] Global test environment set-up. -90: [----------] 12 tests from RotationWorks/RotationTest -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 -90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: trr version: GMX_trn_file (single precision) -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -571580948 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.021 0.011 198.9 -90: (ns/day) (hour/ns) -90: Performance: 421.118 0.057 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (18 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 -90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1080296466 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.016 0.008 198.9 -90: (ns/day) (hour/ns) -90: Performance: 555.007 0.043 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (14 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 -90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -38830122 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.016 0.008 199.1 -90: (ns/day) (hour/ns) -90: Performance: 550.774 0.044 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (13 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 -90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to 1725628159 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.017 0.009 198.5 -90: (ns/day) (hour/ns) -90: Performance: 511.500 0.047 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (14 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 -90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1092633613 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.015 0.008 198.4 -90: (ns/day) (hour/ns) -90: Performance: 577.971 0.042 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (13 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 -90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to 1979567615 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.016 0.008 198.9 -90: (ns/day) (hour/ns) -90: Performance: 542.825 0.044 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (14 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 -90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -67149825 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.021 0.011 198.6 -90: (ns/day) (hour/ns) -90: Performance: 422.259 0.057 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (16 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 -90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -95099186 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.017 0.009 199.1 -90: (ns/day) (hour/ns) -90: Performance: 516.222 0.046 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (14 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 -90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to 1606267903 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.018 0.009 199.1 -90: (ns/day) (hour/ns) -90: Performance: 500.097 0.048 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (14 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 -90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -37 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.019 0.009 199.3 -90: (ns/day) (hour/ns) -90: Performance: 473.733 0.051 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (15 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 -90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -98721 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.019 0.010 199.3 -90: (ns/day) (hour/ns) -90: Performance: 467.180 0.051 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (15 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 -90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -16012810 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.018 0.009 199.2 -90: (ns/day) (hour/ns) -90: Performance: 483.829 0.050 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (14 ms) -90: [----------] 12 tests from RotationWorks/RotationTest (181 ms total) -90: -90: [----------] Global test environment tear-down -90: [==========] 12 tests from 1 test suite ran. (201 ms total) -90: [ PASSED ] 12 tests. -90/92 Test #90: MdrunRotationTests ........................ Passed 0.21 sec -test 91 - Start 91: MdrunSimulatorComparison - -91: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" -91: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -91: Test timeout computed to be: 600 -91: [==========] Running 0 tests from 0 test suites. -91: [==========] 0 tests from 0 test suites ran. (0 ms total) -91: [ PASSED ] 0 tests. -91: -91: YOU HAVE 82 DISABLED TESTS -91: -91/92 Test #91: MdrunSimulatorComparison .................. Passed 0.01 sec -test 92 - Start 92: MdrunVirtualSiteTests - -92: Test command: /build/reproducible-path/gromacs-2025.3/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" -92: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests -92: Test timeout computed to be: 600 -92: [==========] Running 37 tests from 2 test suites. -92: [----------] Global test environment set-up. -92: [----------] 1 test from VirtualSiteVelocityTest -92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect -92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) -92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) -92: -92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 2.3%. -92: The balanceable part of the MD step is 37%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.8%. -92: -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.016 0.008 198.7 -92: (ns/day) (hour/ns) -92: Performance: 94.219 0.255 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: trr version: GMX_trn_file (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (15 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 3.8%. -92: The balanceable part of the MD step is 37%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 1.4%. -92: -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.014 0.007 195.1 -92: (ns/day) (hour/ns) -92: Performance: 110.944 0.216 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (13 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 3.7%. -92: The balanceable part of the MD step is 33%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 1.2%. -92: -92: -92: NOTE: 45 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.012 0.006 197.2 -92: (ns/day) (hour/ns) -92: Performance: 122.769 0.195 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (12 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.007 197.3 -92: (ns/day) (hour/ns) -92: Performance: 119.532 0.201 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (16 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 45 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.011 0.006 197.3 -92: (ns/day) (hour/ns) -92: Performance: 134.303 0.179 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (15 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.012 0.006 197.5 -92: (ns/day) (hour/ns) -92: Performance: 123.280 0.195 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (16 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.006 197.7 -92: (ns/day) (hour/ns) -92: Performance: 119.734 0.200 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (16 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.011 0.006 196.4 -92: (ns/day) (hour/ns) -92: Performance: 138.675 0.173 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (15 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.012 0.006 197.3 -92: (ns/day) (hour/ns) -92: Performance: 122.742 0.196 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (15 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 1.2%. -92: The balanceable part of the MD step is 36%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.4%. -92: -92: -92: NOTE: 47 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.020 0.010 198.4 -92: (ns/day) (hour/ns) -92: Performance: 78.255 0.307 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (15 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 0.6%. -92: The balanceable part of the MD step is 37%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.2%. -92: -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.006 198.1 -92: (ns/day) (hour/ns) -92: Performance: 121.027 0.198 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (11 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 47 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.015 0.008 197.3 -92: (ns/day) (hour/ns) -92: Performance: 101.504 0.236 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (17 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 47 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.032 0.016 198.7 -92: (ns/day) (hour/ns) -92: Performance: 48.457 0.495 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (54 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.023 0.012 198.3 -92: (ns/day) (hour/ns) -92: Performance: 66.703 0.360 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (118 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.018 0.009 197.6 -92: (ns/day) (hour/ns) -92: Performance: 87.801 0.273 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (20 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.015 0.008 197.5 -92: (ns/day) (hour/ns) -92: Performance: 102.070 0.235 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (18 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 45 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.012 0.006 197.6 -92: (ns/day) (hour/ns) -92: Performance: 127.457 0.188 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (16 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.006 197.7 -92: (ns/day) (hour/ns) -92: Performance: 120.648 0.199 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (16 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.006 197.3 -92: (ns/day) (hour/ns) -92: Performance: 122.385 0.196 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (18 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.014 0.007 198.5 -92: (ns/day) (hour/ns) -92: Performance: 108.199 0.222 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (19 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.013 0.007 198.4 -92: (ns/day) (hour/ns) -92: Performance: 114.803 0.209 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (19 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) -92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (487 ms total) -92: -92: [----------] Global test environment tear-down -92: [==========] 37 tests from 2 test suites ran. (512 ms total) -92: [ PASSED ] 37 tests. -92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 0.52 sec - -100% tests passed, 0 tests failed out of 92 - -Label Time Summary: -GTest = 213.25 sec*proc (90 tests) -IntegrationTest = 123.97 sec*proc (29 tests) -MpiTest = 100.59 sec*proc (21 tests) -QuickGpuTest = 62.23 sec*proc (23 tests) -SlowGpuTest = 120.59 sec*proc (14 tests) -SlowTest = 76.21 sec*proc (14 tests) -UnitTest = 13.07 sec*proc (47 tests) - -Total Test time (real) = 125.17 sec -/usr/bin/make -j40 -C build/basic-dp tests -make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 -/usr/bin/make -f CMakeFiles/Makefile2 tests -make[2]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles 78 -/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend -/usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" -/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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/build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options 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directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 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-D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 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-make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 0%] Built target energyanalysis -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 0%] Built target scanner -[ 0%] Built target linearalgebra -[ 1%] Built target tng_io_obj -/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" -[ 2%] Built target options -[ 5%] Built target thread_mpi -[ 5%] Built target release-version-info -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 6%] Built target pulling -/usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment 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api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib 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-/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend -/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/tests/interactivetest.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" 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/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp -/usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/alignedallocator.cpp -/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build -/usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser 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src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp -/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp 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cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/compat/tests/mp11.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 64%] Built target plumed_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/tests/kernelsetup.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 64%] Built target applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/moduletest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constr.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 -[ 64%] Built target taskassignment-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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-Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 65%] Built target fft-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/booltype.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 -cd 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/bitmask32.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp -[ 65%] Built target nblib_test_infrastructure -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include 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directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/mtop.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/symtab.cpp -[ 66%] Built target mdspan-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/topsort.cpp -cd 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 66%] Built target nonbonded-fep-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/forcebuffers.cpp -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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target awh-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/tests/simd_math.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/math/tests/densityfittingforce.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/genion.cpp -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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target listed_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 70%] Built target pdb2gmx2-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 71%] Built target tool-test-with-leaks -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/tools/tests/convert-tpr.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/tpitest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/xvgio.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/settle.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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-/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/periodicactions.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/settletestrunners.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/periodicactions_coupling.cpp -[ 80%] Built target mdrun-single-rank-algorithms-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 80%] Built target mdrun-io-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/shake.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/periodicactions_basic.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 80%] Built target minimize-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/pull_rotation.cpp -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/typetraits.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -isystem 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/integrator.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/status.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c 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"CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -[ 80%] Built target mdrun-mpi-pme-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/stopsignaler.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 82%] Built target fileio-test -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" -[ 82%] Built target mdrun-non-integrator-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/system.cpp -/usr/bin/make -f 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build -/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/util/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/gmxcalculator.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/bondtypes.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/util/tests/setup.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp -[ 82%] Built target mdrun-coordination-coupling-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E 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/usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/kernels.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 83%] Built target workflow-details-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 84%] Built target mdrun-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/filenm.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/typetests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 87%] Built target mdlib-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/calculator.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem 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/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/pargs.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 87%] Built target nblib-tpr-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/shiftforces.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/transformations.cpp -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 87%] Built target gmxapi-test -/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests/helpmanager.cpp -/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests/arraydata.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 87%] Built target nblib-util-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 87%] Built target mdrun-simulator-comparison-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 88%] Built target nblib-integration-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/gyrate.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 88%] Built target mdrun-vsites-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/hbond.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 88%] Built target mdrun-rotation-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/unionfind.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 -[ 89%] Built target mdrun-multisim-replex-equivalence-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 91%] Built target mdrunutility-mpi-test -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 92%] Built target utility-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 93%] Built target onlinehelp-test -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 93%] Built target plumed_md-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 93%] Built target selection-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 94%] Built target commandline-test -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 94%] Built target mdrun-pull-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 94%] Built target analysisdata-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" 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directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 97%] Built target nblib-setup-test -[ 97%] Built target nblib-listed-forces-test -/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 97%] Built target nblib-tests -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" 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"CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 98%] Built target trajectoryanalysis-test -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[100%] Built target math-test -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[100%] Built target tests -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles 0 -make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -(cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/basic-dp/lib ctest -V) -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/basic-dp/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/basic-dp/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/basic-dp/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/basic-dp/DartConfiguration.tcl -Test project /build/reproducible-path/gromacs-2025.3/build/basic-dp -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -test 1 - Start 1: GmxapiExternalInterfaceTests - -1: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" -1: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests -1: Test timeout computed to be: 600 -1: [==========] Running 9 tests from 1 test suite. -1: [----------] Global test environment set-up. -1: [----------] 9 tests from GmxApiTest -1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to -268790150 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 3.620 1.810 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.280 85.822 -1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (2502 ms) -1: [ RUN ] GmxApiTest.RunnerBasicMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to 752271061 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.966 2.983 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.170 141.417 -1: [ OK ] GmxApiTest.RunnerBasicMD (3295 ms) -1: [ RUN ] GmxApiTest.RunnerReinitialize -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: -1: Received the remote INT/TERM signal, stopping within 200 steps -1: -1: Setting the LD random seed to -605393957 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 2.323 1.162 200.0 -1: (ns/day) (hour/ns) -1: Performance: 3.051 7.867 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 5.053 2.527 200.0 -1: (ns/day) (hour/ns) -1: Performance: 1.403 17.111 -1: [ OK ] GmxApiTest.RunnerReinitialize (4671 ms) -1: [ RUN ] GmxApiTest.RunnerChainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to 1979047919 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.046 2.023 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.250 95.918 -1: trr version: GMX_trn_file (double precision) -1: -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Setting nsteps to 4 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -1: Input file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 2 -1: Runtime for the run 0.00390625 ps -1: Run end step 2 -1: Run end time 0.00390625 ps -1: -1: -1: Output file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 4 -1: Runtime for the run 0.0078125 ps -1: Run end step 4 -1: Run end time 0.0078125 ps -1: -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 3.221 1.611 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.314 76.352 -1: -1: [ OK ] GmxApiTest.RunnerChainedMD (4390 ms) -1: [ RUN ] GmxApiTest.Status -1: [ OK ] GmxApiTest.Status (0 ms) -1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: Setting the LD random seed to -16777281 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 3.421 1.711 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.493 48.660 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps -1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 -1: -1: -1: Using 1 MPI thread -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 3.617 1.809 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.187 128.607 -1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4254 ms) -1: [ RUN ] GmxApiTest.SystemConstruction -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Setting the LD random seed to -705189889 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: [ OK ] GmxApiTest.SystemConstruction (483 ms) -1: [ RUN ] GmxApiTest.SaneVersionComparisons -1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) -1: [ RUN ] GmxApiTest.VersionNamed0_1_Features -1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) -1: [----------] 9 tests from GmxApiTest (19598 ms total) -1: -1: [----------] Global test environment tear-down -1: [==========] 9 tests from 1 test suite ran. (19621 ms total) -1: [ PASSED ] 9 tests. - 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 19.64 sec -test 2 - Start 2: GmxapiInternalInterfaceTests - -2: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" -2: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests -2: Test timeout computed to be: 600 -2: [==========] Running 2 tests from 1 test suite. -2: [----------] Global test environment set-up. -2: [----------] 2 tests from GmxApiTest -2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Setting the LD random seed to 1509940214 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (454 ms) -2: [ RUN ] GmxApiTest.CreateApiWorkflow -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Setting the LD random seed to -1275105761 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: [ OK ] GmxApiTest.CreateApiWorkflow (271 ms) -2: [----------] 2 tests from GmxApiTest (725 ms total) -2: -2: [----------] Global test environment tear-down -2: [==========] 2 tests from 1 test suite ran. (745 ms total) -2: [ PASSED ] 2 tests. - 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.76 sec -test 3 - Start 3: NbLibListedForcesTests - -3: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" -3: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/listed_forces/tests -3: Test timeout computed to be: 600 -3: [==========] Running 44 tests from 22 test suites. -3: [----------] Global test environment set-up. -3: [----------] 8 tests from NBlibTest -3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks -3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) -3: [ RUN ] NBlibTest.BondTypesLessThanWorks -3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) -3: [ RUN ] NBlibTest.CanSplitListedWork -3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) -3: [ RUN ] NBlibTest.ListedForceBuffer -3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) -3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct -3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) -3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes -3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) -3: [ RUN ] NBlibTest.EndToEndListedComparison -3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) -3: [ RUN ] NBlibTest.shiftForcesAreCorrect -3: [ OK ] NBlibTest.shiftForcesAreCorrect (14 ms) -3: [----------] 8 tests from NBlibTest (15 ms total) -3: -3: [----------] 1 test from Kernels -3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute -3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) -3: [----------] 1 test from Kernels (0 ms total) -3: -3: [----------] 1 test from FourCenter -3: [ RUN ] FourCenter.ListedForcesProperDihedralTest -3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) -3: [----------] 1 test from FourCenter (0 ms total) -3: -3: [----------] 7 tests from ThreeCenter -3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest -3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest -3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest -3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest -3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest -3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest -3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) -3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest -3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) -3: [----------] 7 tests from ThreeCenter (0 ms total) -3: -3: [----------] 5 tests from TwoCenter -3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest -3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesG96BondTest -3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesCubicBondTest -3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesMorseBondTest -3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) -3: [ RUN ] TwoCenter.ListedForcesFeneBondTest -3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) -3: [----------] 5 tests from TwoCenter (0 ms total) -3: -3: [----------] 5 tests from ListedExampleData -3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces -3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) -3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies -3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) -3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces -3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) -3: [ RUN ] ListedExampleData.CanReduceForces -3: [ OK ] ListedExampleData.CanReduceForces (0 ms) -3: [ RUN ] ListedExampleData.CanReduceEnergies -3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) -3: [----------] 5 tests from ListedExampleData (0 ms total) -3: -3: [----------] 1 test from LinearChainDataFixture -3: [ RUN ] LinearChainDataFixture.Multithreading -3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) -3: [----------] 1 test from LinearChainDataFixture (0 ms total) -3: -3: [----------] 2 tests from ListedShims -3: [ RUN ] ListedShims.ParameterConversion -3: [ OK ] ListedShims.ParameterConversion (0 ms) -3: [ RUN ] ListedShims.GmxToNblibConversion -3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) -3: [----------] 2 tests from ListedShims (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) -3: -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral -3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth -3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) -3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) -3: -3: [----------] 1 test from ListedTransformations -3: [ RUN ] ListedTransformations.SortInteractionIndices -3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) -3: [----------] 1 test from ListedTransformations (0 ms total) -3: -3: [----------] Global test environment tear-down -3: [==========] 44 tests from 22 test suites ran. (17 ms total) -3: [ PASSED ] 44 tests. - 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.03 sec -test 4 - Start 4: NbLibSamplesTestArgon - -4: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/argon-forces-integration -4: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples -4: Test timeout computed to be: 1500 -4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 -4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 -4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 -4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 - 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.01 sec -test 5 - Start 5: NbLibSamplesTestMethaneWater - -5: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/methane-water-integration -5: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples -5: Test timeout computed to be: 1500 -5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 -5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 - 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.01 sec -test 6 - Start 6: NbLibUtilTests - -6: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" -6: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/util/tests -6: Test timeout computed to be: 30 -6: [==========] Running 16 tests from 2 test suites. -6: [----------] Global test environment set-up. -6: [----------] 6 tests from NBlibTest -6: [ RUN ] NBlibTest.isRealValued -6: [ OK ] NBlibTest.isRealValued (0 ms) -6: [ RUN ] NBlibTest.checkNumericValuesHasNan -6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) -6: [ RUN ] NBlibTest.checkNumericValuesHasInf -6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) -6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) -6: [ RUN ] NBlibTest.generateVelocitySize -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.generateVelocitySize (0 ms) -6: [ RUN ] NBlibTest.generateVelocityCheckNumbers -6: Velocities were taken from a Maxwell distribution at 300 K -6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) -6: [----------] 6 tests from NBlibTest (0 ms total) -6: -6: [----------] 10 tests from NblibTraitsUtils -6: [ RUN ] NblibTraitsUtils.FuseTwo -6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) -6: [ RUN ] NblibTraitsUtils.Fuse -6: [ OK ] NblibTraitsUtils.Fuse (0 ms) -6: [ RUN ] NblibTraitsUtils.Repeat -6: [ OK ] NblibTraitsUtils.Repeat (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 -6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 -6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 -6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 -6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) -6: [ RUN ] NblibTraitsUtils.Contains -6: [ OK ] NblibTraitsUtils.Contains (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated -6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) -6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated -6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) -6: [----------] 10 tests from NblibTraitsUtils (0 ms total) -6: -6: [----------] Global test environment tear-down -6: [==========] 16 tests from 2 test suites ran. (0 ms total) -6: [ PASSED ] 16 tests. - 6/92 Test #6: NbLibUtilTests ............................ Passed 0.01 sec -test 7 - Start 7: NbLibSetupTests - -7: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" -7: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests -7: Test timeout computed to be: 600 -7: [==========] Running 57 tests from 3 test suites. -7: [----------] Global test environment set-up. -7: [----------] 41 tests from NBlibTest -7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN -7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) -7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf -7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) -7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN -7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) -7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf -7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) -7: [ RUN ] NBlibTest.CubicBoxWorks -7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) -7: [ RUN ] NBlibTest.BoxEqual -7: [ OK ] NBlibTest.BoxEqual (0 ms) -7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect -7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) -7: [ RUN ] NBlibTest.CanMergeInteractions -7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) -7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed -7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) -7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed -7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) -7: [ RUN ] NBlibTest.PbcHolderWorks -7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) -7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName -7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) -7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule -7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) -7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames -7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) -7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed -7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) -7: [ RUN ] NBlibTest.AtWorks -7: [ OK ] NBlibTest.AtWorks (0 ms) -7: [ RUN ] NBlibTest.AtThrows -7: [ OK ] NBlibTest.AtThrows (0 ms) -7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass -7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) -7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass -7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) -7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName -7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) -7: [ RUN ] NBlibTest.CanAddInteractions -7: [ OK ] NBlibTest.CanAddInteractions (0 ms) -7: [ RUN ] NBlibTest.CanAddUreyBradley -7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) -7: [ RUN ] NBlibTest.TopologyHasNumParticles -7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) -7: [ RUN ] NBlibTest.TopologyHasCharges -7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) -7: [ RUN ] NBlibTest.TopologyHasMasses -7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) -7: [ RUN ] NBlibTest.TopologyHasParticleTypes -7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) -7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds -7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) -7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType -7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) -7: [ RUN ] NBlibTest.TopologyHasExclusions -7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) -7: [ RUN ] NBlibTest.TopologyHasSequencing -7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) -7: [ RUN ] NBlibTest.TopologyCanAggregateBonds -7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) -7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs -7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) -7: [ RUN ] NBlibTest.TopologySequenceIdThrows -7: No particle O-Atom in residue SOL in molecule SOL found -7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) -7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds -7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) -7: [ RUN ] NBlibTest.TopologyListedInteractions -7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) -7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes -7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) -7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows -7: No particle Iron in residue SOL in molecule SOL found -7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) -7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks -7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) -7: [----------] 41 tests from NBlibTest (2 ms total) -7: -7: [----------] 15 tests from NbnxmSetupTest -7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups -7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) -7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM -7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) -7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto -7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) -7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount -7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) -7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain -7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) -7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv -7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) -7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks -7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) -7: [ RUN ] NbnxmSetupTest.updateForcerecWorks -7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) -7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup -7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) -7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM -7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) -7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM -7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) -7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU -7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) -7: [----------] 15 tests from NbnxmSetupTest (0 ms total) -7: -7: [----------] 1 test from VirialsTest -7: [ RUN ] VirialsTest.computeVirialTensorWorks -7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) -7: [----------] 1 test from VirialsTest (0 ms total) -7: -7: [----------] Global test environment tear-down -7: [==========] 57 tests from 3 test suites ran. (2 ms total) -7: [ PASSED ] 57 tests. - 7/92 Test #7: NbLibSetupTests ........................... Passed 0.04 sec -test 8 - Start 8: NbLibTprTests - -8: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" -8: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests -8: Test timeout computed to be: 30 -8: [==========] Running 4 tests from 1 test suite. -8: [----------] Global test environment set-up. -8: [----------] 4 tests from TprReaderTest -8: [ RUN ] TprReaderTest.SimDBTprIsCreated -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.SimDBTprIsCreated (7 ms) -8: [ RUN ] TprReaderTest.Spc2Reads -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Generating 1-4 interactions: fudge = 0.5 -8: Number of degrees of freedom in T-Coupling group System is 9.00 -8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: NVE simulation: will use the initial temperature of 2573.591 K for -8: determining the Verlet buffer size -8: -8: -8: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -8: You are using a plain Coulomb cut-off, which might produce artifacts. -8: You might want to consider using PME electrostatics. -8: -8: -8: -8: There were 4 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -8: Generated 3 of the 3 non-bonded parameter combinations -8: -8: Generated 3 of the 3 1-4 parameter combinations -8: -8: Excluding 2 bonded neighbours molecule type 'SOL' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.Spc2Reads (5 ms) -8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (138 ms) -8: [ RUN ] TprReaderTest.FCfromTprDataWorks -8: -8: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -8: that with the Verlet scheme, nstlist has no effect on the accuracy of -8: your simulation. -8: -8: -8: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: Setting nstcalcenergy (100) equal to nstenergy (4) -8: -8: Number of degrees of freedom in T-Coupling group System is 33.00 -8: -8: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -8: NVE simulation: will use the initial temperature of 68.810 K for -8: determining the Verlet buffer size -8: -8: -8: There were 3 NOTEs -8: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -8: Generated 1 of the 1 non-bonded parameter combinations -8: -8: Excluding 1 bonded neighbours molecule type 'Argon' -8: -8: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -8: -8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -8: -8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -8: -8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -8: -8: Note that mdrun will redetermine rlist based on the actual pair-list setup -8: -8: This run will generate roughly 0 Mb of data -8: [ OK ] TprReaderTest.FCfromTprDataWorks (5 ms) -8: [----------] 4 tests from TprReaderTest (157 ms total) -8: -8: [----------] Global test environment tear-down -8: [==========] 4 tests from 1 test suite ran. (178 ms total) -8: [ PASSED ] 4 tests. - 8/92 Test #8: NbLibTprTests ............................. Passed 0.37 sec -test 9 - Start 9: NbLibIntegrationTests - -9: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" -9: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests -9: Test timeout computed to be: 600 -9: [==========] Running 20 tests from 1 test suite. -9: [----------] Global test environment set-up. -9: [----------] 20 tests from NBlibTest -9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute -9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) -9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect -9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect -9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect -9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect -9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ExpectedNumberOfForces -9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) -9: [ RUN ] NBlibTest.CanIntegrateSystem -9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) -9: [ RUN ] NBlibTest.UpdateChangesForces -9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) -9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect -9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect -9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) -9: [ RUN ] NBlibTest.CanConstructSimulationState -9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN -9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF -9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN -9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) -9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF -9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) -9: [ RUN ] NBlibTest.SimulationStateCanMove -9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) -9: [ RUN ] NBlibTest.SimulationStateCanAssign -9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasBox -9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates -9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) -9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities -9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) -9: [----------] 20 tests from NBlibTest (5 ms total) -9: -9: [----------] Global test environment tear-down -9: [==========] 20 tests from 1 test suite ran. (5 ms total) -9: [ PASSED ] 20 tests. - 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.02 sec -test 10 - Start 10: NbLibIntegratorTests - -10: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" -10: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/tests -10: Test timeout computed to be: 600 -10: [==========] Running 1 test from 1 test suite. -10: [----------] Global test environment set-up. -10: [----------] 1 test from NBlibTest -10: [ RUN ] NBlibTest.IntegratorWorks -10: [ OK ] NBlibTest.IntegratorWorks (0 ms) -10: [----------] 1 test from NBlibTest (0 ms total) -10: -10: [----------] Global test environment tear-down -10: [==========] 1 test from 1 test suite ran. (0 ms total) -10: [ PASSED ] 1 test. -10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.18 sec -test 11 - Start 11: TestUtilsUnitTests - -11: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" -11: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/testutils/tests -11: Test timeout computed to be: 30 -11: [==========] Running 75 tests from 7 test suites. -11: [----------] Global test environment set-up. -11: [----------] 10 tests from InteractiveTestHelperTest -11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession -11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (184 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput -11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput -11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput -11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput -11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) -11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput -11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) -11: [----------] 10 tests from InteractiveTestHelperTest (186 ms total) -11: -11: [----------] 10 tests from NameOfTestFromTupleTest -11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple -11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction -11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat -11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter -11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray -11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) -11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters -11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) -11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) -11: -11: [----------] 3 tests from RefDataFilenameMakerTest -11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction -11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) -11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters -11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) -11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty -11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) -11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) -11: -11: [----------] 37 tests from ReferenceDataTest -11: [ RUN ] ReferenceDataTest.HandlesSimpleData -11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData -11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks -11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesStringBlockData -11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesVectorData -11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceData -11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData -11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) -11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData -11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesIncorrectData -11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType -11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMissingData -11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedData -11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence -11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound -11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnys -11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree -11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey -11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey -11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue -11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType -11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile -11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings -11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace -11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings -11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock -11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices -11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData -11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds -11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds -11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesReadingValues -11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (90 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (175 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (33 ms) -11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries -11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (143 ms) -11: [----------] 37 tests from ReferenceDataTest (447 ms total) -11: -11: [----------] 7 tests from FloatingPointDifferenceTest -11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues -11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues -11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign -11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero -11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences -11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero -11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) -11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN -11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) -11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) -11: -11: [----------] 4 tests from FloatingPointToleranceTest -11: [ RUN ] FloatingPointToleranceTest.UlpTolerance -11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) -11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint -11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) -11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp -11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) -11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance -11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) -11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) -11: -11: [----------] 4 tests from XvgTests -11: [ RUN ] XvgTests.CreateFile -11: [ OK ] XvgTests.CreateFile (137 ms) -11: [ RUN ] XvgTests.CheckMissing -11: [ OK ] XvgTests.CheckMissing (0 ms) -11: [ RUN ] XvgTests.CheckExtra -11: [ OK ] XvgTests.CheckExtra (0 ms) -11: [ RUN ] XvgTests.ReadIncorrect -11: [ OK ] XvgTests.ReadIncorrect (0 ms) -11: [----------] 4 tests from XvgTests (138 ms total) -11: -11: [----------] Global test environment tear-down -11: [==========] 75 tests from 7 test suites ran. (773 ms total) -11: [ PASSED ] 75 tests. -11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.79 sec -test 12 - Start 12: TestUtilsMpiUnitTests - -12: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" -12: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/testutils/tests -12: Test timeout computed to be: 30 -12: [==========] Running 1 test from 1 test suite. -12: [----------] Global test environment set-up. -12: [----------] 1 test from MpiSelfTest -12: [ RUN ] MpiSelfTest.Runs -12: [ OK ] MpiSelfTest.Runs (0 ms) -12: [----------] 1 test from MpiSelfTest (0 ms total) -12: -12: [----------] Global test environment tear-down -12: [==========] 1 test from 1 test suite ran. (0 ms total) -12: [ PASSED ] 1 test. -12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.01 sec -test 13 - Start 13: UtilityUnitTests - -13: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" -13: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests -13: Test timeout computed to be: 30 -13: [==========] Running 420 tests from 65 test suites. -13: [----------] Global test environment set-up. -13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/0.Move -13: [ OK ] AllocatorTest/0.Move (0 ms) -13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/0.Comparison -13: [ OK ] AllocatorTest/0.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/0 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/1.Move -13: [ OK ] AllocatorTest/1.Move (0 ms) -13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/1.Comparison -13: [ OK ] AllocatorTest/1.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/1 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/2.Move -13: [ OK ] AllocatorTest/2.Move (0 ms) -13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/2.Comparison -13: [ OK ] AllocatorTest/2.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/2 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/3.Move -13: [ OK ] AllocatorTest/3.Move (0 ms) -13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/3.Comparison -13: [ OK ] AllocatorTest/3.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/3 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/4.Move -13: [ OK ] AllocatorTest/4.Move (0 ms) -13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/4.Comparison -13: [ OK ] AllocatorTest/4.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/4 (0 ms total) -13: -13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> -13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment -13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment -13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment -13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) -13: [ RUN ] AllocatorTest/5.Move -13: [ OK ] AllocatorTest/5.Move (0 ms) -13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory -13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) -13: [ RUN ] AllocatorTest/5.Comparison -13: [ OK ] AllocatorTest/5.Comparison (0 ms) -13: [----------] 6 tests from AllocatorTest/5 (0 ms total) -13: -13: [----------] 1 test from AllocatorUntypedTest -13: [ RUN ] AllocatorUntypedTest.Comparison -13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) -13: [----------] 1 test from AllocatorUntypedTest (0 ms total) -13: -13: [----------] 4 tests from EmptyArrayRefTest -13: [ RUN ] EmptyArrayRefTest.IsEmpty -13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty -13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) -13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr -13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) -13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull -13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) -13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) -13: -13: [----------] 1 test from EmptyConstArrayRefTest -13: [ RUN ] EmptyConstArrayRefTest.IsEmpty -13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) -13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) -13: -13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef -13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks -13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks -13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks -13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks -13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) -13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks -13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) -13: -13: [----------] 8 tests from BoolType -13: [ RUN ] BoolType.ImplicitConversion -13: [ OK ] BoolType.ImplicitConversion (0 ms) -13: [ RUN ] BoolType.FalseByDefault -13: [ OK ] BoolType.FalseByDefault (0 ms) -13: [ RUN ] BoolType.Assignment -13: [ OK ] BoolType.Assignment (0 ms) -13: [ RUN ] BoolType.Copy -13: [ OK ] BoolType.Copy (0 ms) -13: [ RUN ] BoolType.ArrayRefCanBeCreated -13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) -13: [ RUN ] BoolType.CanBeCastToBool -13: [ OK ] BoolType.CanBeCastToBool (0 ms) -13: [ RUN ] BoolType.HasSizeOfBool -13: [ OK ] BoolType.HasSizeOfBool (0 ms) -13: [ RUN ] BoolType.HasAlignmentOfBool -13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) -13: [----------] 8 tests from BoolType (0 ms total) -13: -13: [----------] 4 tests from ArrayRefFromBoolTypeVector -13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty -13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.Works -13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty -13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) -13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks -13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) -13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) -13: -13: [----------] 7 tests from CStringUtilityTest -13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison -13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) -13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength -13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) -13: [ RUN ] CStringUtilityTest.strip_comment -13: [ OK ] CStringUtilityTest.strip_comment (0 ms) -13: [ RUN ] CStringUtilityTest.upstring -13: [ OK ] CStringUtilityTest.upstring (0 ms) -13: [ RUN ] CStringUtilityTest.ltrim -13: [ OK ] CStringUtilityTest.ltrim (0 ms) -13: [ RUN ] CStringUtilityTest.rtrim -13: [ OK ] CStringUtilityTest.rtrim (0 ms) -13: [ RUN ] CStringUtilityTest.trim -13: [ OK ] CStringUtilityTest.trim (0 ms) -13: [----------] 7 tests from CStringUtilityTest (0 ms total) -13: -13: [----------] 2 tests from DefaultInitializationAllocator -13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization -13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) -13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization -13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) -13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) -13: -13: [----------] 4 tests from EnumerationHelpersTest -13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks -13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) -13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks -13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) -13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe -13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) -13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks -13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) -13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) -13: -13: [----------] 1 test from EnumClassSuitsEnumerationArray -13: [ RUN ] EnumClassSuitsEnumerationArray.Works -13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) -13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) -13: -13: [----------] 18 tests from FixedCapacityVectorTest -13: [ RUN ] FixedCapacityVectorTest.IsEmpty -13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks -13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.PushWorks -13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.PopWorks -13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ResizeWorks -13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ClearWorks -13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks -13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.AtThrows -13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) -13: [ RUN ] FixedCapacityVectorTest.IteratorWorks -13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks -13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks -13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks -13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks -13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks -13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.DataWorks -13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) -13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork -13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) -13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) -13: -13: [----------] 5 tests from InMemorySerializerTest -13: [ RUN ] InMemorySerializerTest.Roundtrip -13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) -13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap -13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap -13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap -13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) -13: [ RUN ] InMemorySerializerTest.SizeIsCorrect -13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) -13: [----------] 5 tests from InMemorySerializerTest (0 ms total) -13: -13: [----------] 4 tests from KeyValueTreeSerializerTest -13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree -13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject -13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays -13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) -13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects -13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) -13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) -13: -13: [----------] 7 tests from TreeValueTransformTest -13: [ RUN ] TreeValueTransformTest.SimpleTransforms -13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) -13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive -13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) -13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject -13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) -13: [ RUN ] TreeValueTransformTest.ObjectFromString -13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) -13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings -13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) -13: [ RUN ] TreeValueTransformTest.ScopedTransformRules -13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) -13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue -13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) -13: [----------] 7 tests from TreeValueTransformTest (0 ms total) -13: -13: [----------] 1 test from TreeValueTransformErrorTest -13: [ RUN ] TreeValueTransformErrorTest.ConversionError -13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) -13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) -13: -13: [----------] 9 tests from ListOfLists -13: [ RUN ] ListOfLists.EmptyListOfListsWorks -13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) -13: [ RUN ] ListOfLists.AppendWorks -13: [ OK ] ListOfLists.AppendWorks (0 ms) -13: [ RUN ] ListOfLists.EmptyListWorks -13: [ OK ] ListOfLists.EmptyListWorks (0 ms) -13: [ RUN ] ListOfLists.AppendAccessWorks -13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) -13: [ RUN ] ListOfLists.ClearWorks -13: [ OK ] ListOfLists.ClearWorks (0 ms) -13: [ RUN ] ListOfLists.OutOfRangeAccessThrows -13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) -13: [ RUN ] ListOfLists.FrontAndBackWork -13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) -13: [ RUN ] ListOfLists.ExtractsAndRestores -13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) -13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset -13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) -13: [----------] 9 tests from ListOfLists (0 ms total) -13: -13: [----------] 7 tests from LoggerTest -13: [ RUN ] LoggerTest.EmptyLoggerWorks -13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) -13: [ RUN ] LoggerTest.LogsToStream -13: [ OK ] LoggerTest.LogsToStream (0 ms) -13: [ RUN ] LoggerTest.LogsToFile -13: [ OK ] LoggerTest.LogsToFile (29 ms) -13: [ RUN ] LoggerTest.LevelFilteringWorks -13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) -13: [ RUN ] LoggerTest.LogsToMultipleStreams -13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) -13: [ RUN ] LoggerTest.LogsToMultipleFiles -13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) -13: [ RUN ] LoggerTest.LogsToStreamAndFile -13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) -13: [----------] 7 tests from LoggerTest (30 ms total) -13: -13: [----------] 7 tests from MessageStringCollectorTest -13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext -13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext -13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages -13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally -13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally -13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct -13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) -13: [ RUN ] MessageStringCollectorTest.CanMoveAssign -13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) -13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) -13: -13: [----------] 1 test from PathTest -13: [ RUN ] PathTest.StripSourcePrefixWorks -13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) -13: [----------] 1 test from PathTest (0 ms total) -13: -13: [----------] 2 tests from PhysicalNodeCommunicatorTest -13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -13: -13: [----------] 5 tests from Range -13: [ RUN ] Range.EmptyRangeWorks -13: [ OK ] Range.EmptyRangeWorks (0 ms) -13: [ RUN ] Range.NonEmptyRangeWorks -13: [ OK ] Range.NonEmptyRangeWorks (0 ms) -13: [ RUN ] Range.BeginEnd -13: [ OK ] Range.BeginEnd (0 ms) -13: [ RUN ] Range.IsInRangeWorks -13: [ OK ] Range.IsInRangeWorks (0 ms) -13: [ RUN ] Range.IteratorWorks -13: [ OK ] Range.IteratorWorks (0 ms) -13: [----------] 5 tests from Range (0 ms total) -13: -13: [----------] 3 tests from ScopeGuardTest -13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit -13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) -13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers -13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) -13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions -13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) -13: [----------] 3 tests from ScopeGuardTest (0 ms total) -13: -13: [----------] 7 tests from StringConvert -13: [ RUN ] StringConvert.NoResultFromEptyString -13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) -13: [ RUN ] StringConvert.ThreeFloatsSuccessfully -13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) -13: [ RUN ] StringConvert.OneIntSucessfully -13: [ OK ] StringConvert.OneIntSucessfully (0 ms) -13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows -13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) -13: [ RUN ] StringConvert.ThrowsWhenWrongSize -13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) -13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows -13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) -13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay -13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) -13: [----------] 7 tests from StringConvert (0 ms total) -13: -13: [----------] 7 tests from StringToEnumValueConverterTest -13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping -13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping -13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) -13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks -13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) -13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) -13: -13: [----------] 9 tests from StringUtilityTest -13: [ RUN ] StringUtilityTest.StartsWith -13: [ OK ] StringUtilityTest.StartsWith (0 ms) -13: [ RUN ] StringUtilityTest.EndsWith -13: [ OK ] StringUtilityTest.EndsWith (0 ms) -13: [ RUN ] StringUtilityTest.StripSuffixIfPresent -13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) -13: [ RUN ] StringUtilityTest.StripString -13: [ OK ] StringUtilityTest.StripString (0 ms) -13: [ RUN ] StringUtilityTest.SplitString -13: [ OK ] StringUtilityTest.SplitString (0 ms) -13: [ RUN ] StringUtilityTest.SplitDelimitedString -13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) -13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString -13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) -13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive -13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) -13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength -13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) -13: [----------] 9 tests from StringUtilityTest (0 ms total) -13: -13: [----------] 2 tests from FormatStringTest -13: [ RUN ] FormatStringTest.HandlesBasicFormatting -13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) -13: [ RUN ] FormatStringTest.HandlesLongStrings -13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) -13: [----------] 2 tests from FormatStringTest (0 ms total) -13: -13: [----------] 1 test from StringFormatterTest -13: [ RUN ] StringFormatterTest.HandlesBasicFormatting -13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) -13: [----------] 1 test from StringFormatterTest (0 ms total) -13: -13: [----------] 1 test from formatAndJoinTest -13: [ RUN ] formatAndJoinTest.Works -13: [ OK ] formatAndJoinTest.Works (0 ms) -13: [----------] 1 test from formatAndJoinTest (0 ms total) -13: -13: [----------] 1 test from JoinStringsTest -13: [ RUN ] JoinStringsTest.Works -13: [ OK ] JoinStringsTest.Works (0 ms) -13: [----------] 1 test from JoinStringsTest (0 ms total) -13: -13: [----------] 6 tests from ReplaceAllTest -13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings -13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesNoMatches -13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds -13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches -13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries -13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) -13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches -13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) -13: [----------] 6 tests from ReplaceAllTest (0 ms total) -13: -13: [----------] 10 tests from TextLineWrapperTest -13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings -13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace -13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines -13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectly -13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks -13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesIndent -13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines -13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent -13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) -13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter -13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) -13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace -13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) -13: [----------] 10 tests from TextLineWrapperTest (0 ms total) -13: -13: [----------] 1 test from CompileTimeStringJoin -13: [ RUN ] CompileTimeStringJoin.Works -13: [ OK ] CompileTimeStringJoin.Works (0 ms) -13: [----------] 1 test from CompileTimeStringJoin (0 ms total) -13: -13: [----------] 3 tests from TemplateMPTest -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) -13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool -13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) -13: [----------] 3 tests from TemplateMPTest (0 ms total) -13: -13: [----------] 6 tests from TextWriterTest -13: [ RUN ] TextWriterTest.WritesLines -13: [ OK ] TextWriterTest.WritesLines (0 ms) -13: [ RUN ] TextWriterTest.WritesLinesInParts -13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) -13: [ RUN ] TextWriterTest.WritesWrappedLines -13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) -13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper -13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) -13: [ RUN ] TextWriterTest.TracksNewlines -13: [ OK ] TextWriterTest.TracksNewlines (0 ms) -13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace -13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) -13: [----------] 6 tests from TextWriterTest (0 ms total) -13: -13: [----------] 1 test from TypeTraitsTest -13: [ RUN ] TypeTraitsTest.IsIntegralConstant -13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) -13: [----------] 1 test from TypeTraitsTest (0 ms total) -13: -13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) -13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 -13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) -13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) -13: -13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) -13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 -13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) -13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) -13: -13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) -13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 -13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) -13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) -13: -13: [----------] 11 tests from WithInputPaths/PathSearchTest -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) -13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 -13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) -13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) -13: -13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) -13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 -13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) -13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) -13: -13: [----------] Global test environment tear-down -13: [==========] 420 tests from 65 test suites ran. (38 ms total) -13: [ PASSED ] 420 tests. -13: -13: YOU HAVE 1 DISABLED TEST -13: -13/92 Test #13: UtilityUnitTests .......................... Passed 0.20 sec -test 14 - Start 14: UtilityMpiUnitTests - -14: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" -14: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/utility/tests -14: Test timeout computed to be: 30 -14: [==========] Running 2 tests from 1 test suite. -14: [----------] Global test environment set-up. -14: [----------] 2 tests from PhysicalNodeCommunicatorTest -14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -14: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -14: -14: [----------] Global test environment tear-down -14: [==========] 2 tests from 1 test suite ran. (0 ms total) -14: [ PASSED ] 2 tests. -14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.13 sec -test 15 - Start 15: GmxlibTests - -15: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxlibTests.xml" -15: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests -15: Test timeout computed to be: 30 -15: [==========] Running 78 tests from 2 test suites. -15: [----------] Global test environment set-up. -15: [----------] 72 tests from NBInteraction/NonbondedFepTest -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) -15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 -15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) -15: [----------] 72 tests from NBInteraction/NonbondedFepTest (8 ms total) -15: -15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) -15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 -15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) -15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) -15: -15: [----------] Global test environment tear-down -15: [==========] 78 tests from 2 test suites ran. (8 ms total) -15: [ PASSED ] 78 tests. -15/92 Test #15: GmxlibTests ............................... Passed 0.12 sec -test 16 - Start 16: MdlibUnitTest - -16: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" -16: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests -16: Test timeout computed to be: 30 -16: [==========] Running 1032 tests from 27 test suites. -16: [----------] Global test environment set-up. -16: [----------] 3 tests from EffectiveAtomDensity -16: [ RUN ] EffectiveAtomDensity.VolumeIndependence -16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) -16: [ RUN ] EffectiveAtomDensity.WeightingWorks -16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) -16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell -16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) -16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) -16: -16: [----------] 2 tests from AtomNonbondedAndKineticProperties -16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate -16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) -16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork -16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) -16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) -16: -16: [----------] 1 test from VerletBufferConstraintTest -16: [ RUN ] VerletBufferConstraintTest.EqualMasses -16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) -16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) -16: -16: [----------] 1 test from VerletBufferSize -16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent -16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) -16: [----------] 1 test from VerletBufferSize (0 ms total) -16: -16: [----------] 6 tests from CalcvirTest -16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox -16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew -16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) -16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ -16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) -16: [----------] 6 tests from CalcvirTest (0 ms total) -16: -16: [----------] 2 tests from PrEbinTest -16: [ RUN ] PrEbinTest.HandlesAverages -16: [ OK ] PrEbinTest.HandlesAverages (78 ms) -16: [ RUN ] PrEbinTest.HandlesEmptyAverages -16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) -16: [----------] 2 tests from PrEbinTest (78 ms total) -16: -16: [----------] 3 tests from EnergyDriftTracker -16: [ RUN ] EnergyDriftTracker.emptyWorks -16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) -16: [ RUN ] EnergyDriftTracker.onePointWorks -16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) -16: [ RUN ] EnergyDriftTracker.manyPointsWorks -16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) -16: [----------] 3 tests from EnergyDriftTracker (0 ms total) -16: -16: [----------] 4 tests from ShakeTest -16: [ RUN ] ShakeTest.ConstrainsOneBond -16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) -16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds -16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) -16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom -16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) -16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms -16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) -16: [----------] 4 tests from ShakeTest (0 ms total) -16: -16: [----------] 1 test from NullSignalTest -16: [ RUN ] NullSignalTest.NullSignallerWorks -16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) -16: [----------] 1 test from NullSignalTest (0 ms total) -16: -16: [----------] 7 tests from SignalTest -16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace -16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) -16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace -16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace -16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace -16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) -16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace -16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) -16: [----------] 7 tests from SignalTest (0 ms total) -16: -16: [----------] 13 tests from UpdateGroupsTest -16: [ RUN ] UpdateGroupsTest.WithEthaneUA -16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) -16: [ RUN ] UpdateGroupsTest.WithMethane -16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) -16: [ RUN ] UpdateGroupsTest.WithEthane -16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) -16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane -16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) -16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups -16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite -16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterFourSite -16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) -16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle -16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) -16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle -16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) -16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle -16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) -16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes -16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) -16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid -16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) -16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful -16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) -16: [----------] 13 tests from UpdateGroupsTest (0 ms total) -16: -16: [----------] 1 test from UpdateGroupsCog -16: [ RUN ] UpdateGroupsCog.ComputesCogs -16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) -16: [----------] 1 test from UpdateGroupsCog (0 ms total) -16: -16: [----------] 2 tests from WholeMoleculeTransform -16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole -16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) -16: [ RUN ] WholeMoleculeTransform.HandlesReordering -16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) -16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) -16: -16: [----------] 28 tests from WithParameters/ConstraintsTest -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) -16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 -16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) -16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 -16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) -16: [----------] 28 tests from WithParameters/ConstraintsTest (14 ms total) -16: -16: [----------] 11 tests from WithParameters/EnergyOutputTest -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 -16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file -16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (3 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) -16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 -16: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file -16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (1 ms) -16: [----------] 11 tests from WithParameters/EnergyOutputTest (14 ms total) -16: -16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) -16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 -16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) -16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) -16: -16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) -16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 -16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) -16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) -16: -16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) -16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 -16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) -16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) -16: -16: [----------] 17 tests from WithParameters/LangevinTest -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) -16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 -16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) -16: [----------] 17 tests from WithParameters/LangevinTest (2 ms total) -16: -16: [----------] 16 tests from WithParameters/LeapFrogTest -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) -16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 -16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) -16: [----------] 16 tests from WithParameters/LeapFrogTest (11 ms total) -16: -16: [----------] 140 tests from Cubic/ParrRahmTest -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Cubic/ParrRahmTest (7 ms total) -16: -16: [----------] 140 tests from Rectilinear/ParrRahmTest -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Rectilinear/ParrRahmTest (10 ms total) -16: -16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (7 ms total) -16: -16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (6 ms total) -16: -16: [----------] 140 tests from TruncOct/ParrRahmTest -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 -16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from TruncOct/ParrRahmTest (10 ms total) -16: -16: [----------] 140 tests from Other/ParrRahmTest -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 -16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -16: [----------] 140 tests from Other/ParrRahmTest (11 ms total) -16: -16: [----------] 13 tests from WithParameters/SettleTest -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) -16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 -16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) -16: [----------] 13 tests from WithParameters/SettleTest (5 ms total) -16: -16: [----------] Global test environment tear-down -16: [==========] 1032 tests from 27 test suites ran. (183 ms total) -16: [ PASSED ] 1032 tests. -16/92 Test #16: MdlibUnitTest ............................. Passed 0.44 sec -test 17 - Start 17: AwhTest - -17: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/AwhTest.xml" -17: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/awh/tests -17: Test timeout computed to be: 30 -17: [==========] Running 27 tests from 10 test suites. -17: [----------] Global test environment set-up. -17: [----------] 3 tests from SerializationTest -17: [ RUN ] SerializationTest.CanSerializeDimParams -17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) -17: [ RUN ] SerializationTest.CanSerializeBiasParams -17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) -17: [ RUN ] SerializationTest.CanSerializeAwhParams -17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) -17: [----------] 3 tests from SerializationTest (0 ms total) -17: -17: [----------] 1 test from BiasTest -17: [ RUN ] BiasTest.DetectsCovering -17: [ OK ] BiasTest.DetectsCovering (0 ms) -17: [----------] 1 test from BiasTest (0 ms total) -17: -17: [----------] 1 test from biasGridTest -17: [ RUN ] biasGridTest.neighborhood -17: [ OK ] biasGridTest.neighborhood (0 ms) -17: [----------] 1 test from biasGridTest (0 ms total) -17: -17: [----------] 2 tests from BiasSharingTest -17: [ RUN ] BiasSharingTest.SharingWorks -17: [ OK ] BiasSharingTest.SharingWorks (0 ms) -17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks -17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (1 ms) -17: [----------] 2 tests from BiasSharingTest (2 ms total) -17: -17: [----------] 2 tests from BiasFepLambdaStateTest -17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering -17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (2 ms) -17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy -17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) -17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) -17: -17: [----------] 8 tests from WithParameters/BiasTest -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) -17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 -17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) -17: [----------] 8 tests from WithParameters/BiasTest (3 ms total) -17: -17: [----------] 2 tests from WithParameters/BiasStateTest -17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 -17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) -17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 -17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) -17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) -17: -17: [----------] 1 test from WithParameters/UserInputTest -17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 -17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) -17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) -17: -17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) -17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 -17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) -17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (16 ms total) -17: -17: [----------] 3 tests from WithParameters/FrictionMetricTest -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) -17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 -17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) -17: [----------] 3 tests from WithParameters/FrictionMetricTest (13 ms total) -17: -17: [----------] Global test environment tear-down -17: [==========] 27 tests from 10 test suites ran. (41 ms total) -17: [ PASSED ] 27 tests. -17/92 Test #17: AwhTest ................................... Passed 0.09 sec -test 18 - Start 18: DensityFittingAppliedForcesUnitTest - -18: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" -18: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests -18: Test timeout computed to be: 30 -18: [==========] Running 18 tests from 4 test suites. -18: [----------] Global test environment set-up. -18: [----------] 2 tests from DensityFittingTest -18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows -18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) -18: [ RUN ] DensityFittingTest.SingleAtom -18: [ OK ] DensityFittingTest.SingleAtom (0 ms) -18: [----------] 2 tests from DensityFittingTest (0 ms total) -18: -18: [----------] 7 tests from DensityFittingAmplitudeLookupTest -18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity -18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge -18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses -18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign -18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct -18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign -18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) -18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct -18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) -18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) -18: -18: [----------] 1 test from DensityFittingForceProviderState -18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving -18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) -18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) -18: -18: [----------] 8 tests from DensityFittingOptionsTest -18: [ RUN ] DensityFittingOptionsTest.DefaultParameters -18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive -18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive -18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive -18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) -18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup -18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt -18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) -18: [ RUN ] DensityFittingOptionsTest.KvtToInternal -18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) -18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent -18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) -18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) -18: -18: [----------] Global test environment tear-down -18: [==========] 18 tests from 4 test suites ran. (1 ms total) -18: [ PASSED ] 18 tests. -18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.01 sec -test 19 - Start 19: QMMMAppliedForcesUnitTest - -19: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" -19: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests -19: Test timeout computed to be: 30 -19: [==========] Running 21 tests from 5 test suites. -19: [----------] Global test environment set-up. -19: [----------] 3 tests from QMMMInputGeneratorTest -19: [ RUN ] QMMMInputGeneratorTest.CanConstruct -19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) -19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink -19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) -19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink -19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) -19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) -19: -19: [----------] 7 tests from QMMMTopologyPreprocessorTest -19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct -19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to -691070985 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (94 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to -1214582817 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (19 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 21.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to 1069285113 -19: -19: Generated 10 of the 10 non-bonded parameter combinations -19: -19: Generated 10 of the 10 1-4 parameter combinations -19: -19: Excluding 2 bonded neighbours molecule type 'SOL' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -19: Analysing residue names: -19: There are: 4 Water residues -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (200 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: Number of degrees of freedom in T-Coupling group rest is 63.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: NVE simulation: will use the initial temperature of 129.093 K for -19: determining the Verlet buffer size -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to 1461124087 -19: -19: Generated 2145 of the 2145 non-bonded parameter combinations -19: -19: Generated 2145 of the 2145 1-4 parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -19: Analysing residue names: -19: There are: 3 Protein residues -19: Analysing Protein... -19: -19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -19: -19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -19: -19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -19: -19: Note that mdrun will redetermine rlist based on the actual pair-list setup -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (150 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Generating 1-4 interactions: fudge = 0.5 -19: -19: NOTE 2 [file unknown]: -19: You are using constraints on all bonds, whereas the forcefield has been -19: parametrized only with constraints involving hydrogen atoms. We suggest -19: using constraints = h-bonds instead, this will also improve performance. -19: -19: -19: NOTE 3 [file unknown]: -19: For energy conservation with LINCS, lincs_iter should be 2 or larger. -19: -19: -19: Number of degrees of freedom in T-Coupling group rest is 42.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: NVE simulation: will use the initial temperature of 193.640 K for -19: determining the Verlet buffer size -19: -19: -19: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 5 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to -591043 -19: -19: Generated 2145 of the 2145 non-bonded parameter combinations -19: -19: Generated 2145 of the 2145 1-4 parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -19: -19: turning all bonds into constraints... -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -19: Analysing residue names: -19: There are: 3 Protein residues -19: Analysing Protein... -19: -19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -19: -19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -19: -19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -19: -19: Note that mdrun will redetermine rlist based on the actual pair-list setup -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (197 ms) -19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites -19: -19: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: For a correct single-point energy evaluation with nsteps = 0, use -19: continuation = yes to avoid constraining the input coordinates. -19: -19: Number of degrees of freedom in T-Coupling group rest is 45.00 -19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -19: -19: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: NVE simulation with an initial temperature of zero: will use a Verlet -19: buffer of 10%. Check your energy drift! -19: -19: -19: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -19: You are using a plain Coulomb cut-off, which might produce artifacts. -19: You might want to consider using PME electrostatics. -19: -19: -19: -19: There were 3 NOTEs -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -19: Setting the LD random seed to 654245795 -19: -19: Generated 3 of the 6 non-bonded parameter combinations -19: -19: Excluding 3 bonded neighbours molecule type 'VSTEST' -19: -19: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -19: -19: Cleaning up constraints and constant bonded interactions with virtual sites -19: Analysing residue names: -19: There are: 1 Other residues -19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -19: -19: This run will generate roughly 0 Mb of data -19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (185 ms) -19: [----------] 7 tests from QMMMTopologyPreprocessorTest (849 ms total) -19: -19: [----------] 9 tests from QMMMOptionsTest -19: [ RUN ] QMMMOptionsTest.DefaultParameters -19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) -19: [ RUN ] QMMMOptionsTest.OptionSetsActive -19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) -19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive -19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive -19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) -19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup -19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) -19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack -19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) -19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing -19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) -19: [----------] 9 tests from QMMMOptionsTest (1 ms total) -19: -19: [----------] 1 test from QMMMForceProviderTest -19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot -19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) -19: [----------] 1 test from QMMMForceProviderTest (0 ms total) -19: -19: [----------] 1 test from QMMMTest -19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows -19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) -19: [----------] 1 test from QMMMTest (0 ms total) -19: -19: [----------] Global test environment tear-down -19: [==========] 21 tests from 5 test suites ran. (851 ms total) -19: [ PASSED ] 21 tests. -19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.86 sec -test 20 - Start 20: ColvarsAppliedForcesUnitTest - -20: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" -20: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests -20: Test timeout computed to be: 30 -20: [==========] Running 16 tests from 4 test suites. -20: [----------] Global test environment set-up. -20: [----------] 1 test from ColvarsTest -20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows -20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) -20: [----------] 1 test from ColvarsTest (0 ms total) -20: -20: [----------] 6 tests from ColvarsOptionsTest -20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive -20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive -20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive -20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.OptionSetsActive -20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) -20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to 1744549756 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (4 ms) -20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename -20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) -20: [----------] 6 tests from ColvarsOptionsTest (4 ms total) -20: -20: [----------] 4 tests from ColvarsPreProcessorTest -20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -1227379461 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (33 ms) -20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -1409290640 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (253 ms) -20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -1275209729 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (161 ms) -20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -571053193 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (192 ms) -20: [----------] 4 tests from ColvarsPreProcessorTest (641 ms total) -20: -20: [----------] 5 tests from ColvarsForceProviderTest -20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot -20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) -20: [ RUN ] ColvarsForceProviderTest.SimpleInputs -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -406848131 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.SimpleInputs (19 ms) -20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -34669705 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (258 ms) -20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 21.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: NVE simulation with an initial temperature of zero: will use a Verlet -20: buffer of 10%. Check your energy drift! -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to 1996450655 -20: -20: Generated 10 of the 10 non-bonded parameter combinations -20: -20: Generated 10 of the 10 1-4 parameter combinations -20: -20: Excluding 2 bonded neighbours molecule type 'SOL' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -20: Analysing residue names: -20: There are: 4 Water residues -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (48 ms) -20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine -20: -20: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: For a correct single-point energy evaluation with nsteps = 0, use -20: continuation = yes to avoid constraining the input coordinates. -20: -20: Generating 1-4 interactions: fudge = 0.5 -20: Number of degrees of freedom in T-Coupling group rest is 66.00 -20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -20: -20: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: NVE simulation: will use the initial temperature of 300.368 K for -20: determining the Verlet buffer size -20: -20: -20: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -20: You are using a plain Coulomb cut-off, which might produce artifacts. -20: You might want to consider using PME electrostatics. -20: -20: -20: -20: There were 3 NOTEs -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -20: Setting the LD random seed to -262490 -20: -20: Generated 2211 of the 2211 non-bonded parameter combinations -20: -20: Generated 2211 of the 2211 1-4 parameter combinations -20: -20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -20: -20: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -20: Analysing residue names: -20: There are: 2 Protein residues -20: Analysing Protein... -20: -20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -20: -20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -20: -20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -20: -20: Note that mdrun will redetermine rlist based on the actual pair-list setup -20: -20: This run will generate roughly 0 Mb of data -20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (258 ms) -20: [----------] 5 tests from ColvarsForceProviderTest (586 ms total) -20: -20: [----------] Global test environment tear-down -20: [==========] 16 tests from 4 test suites ran. (1233 ms total) -20: [ PASSED ] 16 tests. -20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 1.33 sec -test 21 - Start 21: PlumedAppliedForcesUnitTests - -21: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" -21: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests -21: Test timeout computed to be: 30 -21: [==========] Running 8 tests from 1 test suite. -21: [----------] Global test environment set-up. -21: [----------] 8 tests from PlumedOptionsTest -21: [ RUN ] PlumedOptionsTest.defaultConstructor -21: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) -21: [ RUN ] PlumedOptionsTest.setTimeStep -21: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) -21: [ RUN ] PlumedOptionsTest.setStartingBehavior -21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) -21: [ RUN ] PlumedOptionsTest.setPlumedFile -21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) -21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet -21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) -21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data -21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) -21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant -21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) -21: [ RUN ] PlumedOptionsTest.setTopology -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 21.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: -21: NOTE 2 [file angles1.top, line 72]: -21: In moleculetype 'butane' 4 atoms are not bound by a potential or -21: constraint to any other atom in the same moleculetype. Although -21: technically this might not cause issues in a simulation, this often means -21: that the user forgot to add a bond/potential/constraint or put multiple -21: molecules in the same moleculetype definition by mistake. Run with -v to -21: get information for each atom. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -21: NVE simulation: will use the initial temperature of 238.919 K for -21: determining the Verlet buffer size -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 17493.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -21: NVE simulation: will use the initial temperature of 67.983 K for -21: determining the Verlet buffer size -21: -21: -21: There were 2 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: There were 2 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 9.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 18.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: NVE simulation: will use the initial temperature of 135.187 K for -21: determining the Verlet buffer size -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -21: Setting the LD random seed to -277883817 -21: -21: Generated 10 of the 10 non-bonded parameter combinations -21: -21: Generated 10 of the 10 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Water residues -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -1056130 -21: -21: Generated 3 of the 3 non-bonded parameter combinations -21: -21: Excluding 3 bonded neighbours molecule type 'butane' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/angles1.gro' -21: Analysing residue names: -21: There are: 1 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -84279821 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'Argon' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon5832.gro' -21: Analysing residue names: -21: There are: 5832 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -573055233 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonA' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonB' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonC' -21: -21: Excluding 1 bonded neighbours molecule type 'ArgonD' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -138617353 -21: -21: Generated 1 of the 1 non-bonded parameter combinations -21: -21: Excluding 1 bonded neighbours molecule type 'Dipole' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -21: Analysing residue names: -21: There are: 2 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: This run will generate roughly 0 Mb of data -21: Setting the LD random seed to -30810467 -21: -21: Generated 331705 of the 331705 non-bonded parameter combinations -21: -21: Generated 331705 of the 331705 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Excluding 3 bonded neighbours molecule type 'methane' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -21: Analysing residue names: -21: There are: 1 Water residues -21: There are: 1 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] PlumedOptionsTest.setTopology (1377 ms) -21: [----------] 8 tests from PlumedOptionsTest (1377 ms total) -21: -21: [----------] Global test environment tear-down -21: [==========] 8 tests from 1 test suite ran. (1377 ms total) -21: [ PASSED ] 8 tests. -21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 1.39 sec -test 22 - Start 22: PlumedMDTests - -22: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" -22: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests -22: Test timeout computed to be: 600 -22: [==========] Running 2 tests from 1 test suite. -22: [----------] Global test environment set-up. -22: [----------] 2 tests from SimplePlumedMD/PlumedRun -22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 -22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) -22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) -22: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) -22: -22: [----------] Global test environment tear-down -22: [==========] 2 tests from 1 test suite ran. (31 ms total) -22: [ PASSED ] 0 tests. -22: [ SKIPPED ] 2 tests, listed below: -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 -22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -22/92 Test #22: PlumedMDTests ............................. Passed 0.06 sec -test 23 - Start 23: NNPotAppliedForcesUnitTest - -23: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" -23: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests -23: Test timeout computed to be: 30 -23: [==========] Running 12 tests from 4 test suites. -23: [----------] Global test environment set-up. -23: [----------] 1 test from NNPotTest -23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows -23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) -23: [----------] 1 test from NNPotTest (0 ms total) -23: -23: [----------] 5 tests from NNPotOptionsTest -23: [ RUN ] NNPotOptionsTest.DefaultParameters -23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) -23: [ RUN ] NNPotOptionsTest.OptionSetsActive -23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) -23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive -23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive -23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) -23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack -23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) -23: [----------] 5 tests from NNPotOptionsTest (0 ms total) -23: -23: [----------] 5 tests from NNPotTopologyPreprocessorTest -23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct -23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 21.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Setting the LD random seed to 2146817023 -23: -23: Generated 10 of the 10 non-bonded parameter combinations -23: -23: Generated 10 of the 10 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Water residues -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 21.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Setting the LD random seed to -96341 -23: -23: Generated 10 of the 10 non-bonded parameter combinations -23: -23: Generated 10 of the 10 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Water residues -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (134 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 63.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: NVE simulation: will use the initial temperature of 129.093 K for -23: determining the Verlet buffer size -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Setting the LD random seed to -69207173 -23: -23: Generated 2145 of the 2145 non-bonded parameter combinations -23: -23: Generated 2145 of the 2145 1-4 parameter combinations -23: -23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -23: Analysing residue names: -23: There are: 3 Protein residues -23: Analysing Protein... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (129 ms) -23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: -23: NOTE 2 [file unknown]: -23: You are using constraints on all bonds, whereas the forcefield has been -23: parametrized only with constraints involving hydrogen atoms. We suggest -23: using constraints = h-bonds instead, this will also improve performance. -23: -23: -23: NOTE 3 [file unknown]: -23: For energy conservation with LINCS, lincs_iter should be 2 or larger. -23: -23: -23: Number of degrees of freedom in T-Coupling group rest is 42.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: NVE simulation: will use the initial temperature of 193.640 K for -23: determining the Verlet buffer size -23: -23: -23: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 5 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -23: Setting the LD random seed to -4206091 -23: -23: Generated 2145 of the 2145 non-bonded parameter combinations -23: -23: Generated 2145 of the 2145 1-4 parameter combinations -23: -23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -23: -23: turning all bonds into constraints... -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -23: Analysing residue names: -23: There are: 3 Protein residues -23: Analysing Protein... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (399 ms) -23: [----------] 5 tests from NNPotTopologyPreprocessorTest (667 ms total) -23: -23: [----------] 1 test from NNPotForceProviderTest -23: [ RUN ] NNPotForceProviderTest.CanConstruct -23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) -23: [----------] 1 test from NNPotForceProviderTest (0 ms total) -23: -23: [----------] Global test environment tear-down -23: [==========] 12 tests from 4 test suites ran. (668 ms total) -23: [ PASSED ] 12 tests. -23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.70 sec -test 24 - Start 24: AppliedForcesUnitTest - -24: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" -24: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/applied_forces/tests -24: Test timeout computed to be: 30 -24: [==========] Running 3 tests from 1 test suite. -24: [----------] Global test environment set-up. -24: [----------] 3 tests from ElectricFieldTest -24: [ RUN ] ElectricFieldTest.Static -24: [ OK ] ElectricFieldTest.Static (0 ms) -24: [ RUN ] ElectricFieldTest.Oscillating -24: [ OK ] ElectricFieldTest.Oscillating (0 ms) -24: [ RUN ] ElectricFieldTest.Pulsed -24: [ OK ] ElectricFieldTest.Pulsed (0 ms) -24: [----------] 3 tests from ElectricFieldTest (0 ms total) -24: -24: [----------] Global test environment tear-down -24: [==========] 3 tests from 1 test suite ran. (0 ms total) -24: [ PASSED ] 3 tests. -24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.01 sec -test 25 - Start 25: ListedForcesTest - -25: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" -25: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/listed_forces/tests -25: Test timeout computed to be: 30 -25: [==========] Running 132 tests from 9 test suites. -25: [----------] Global test environment set-up. -25: [----------] 24 tests from Bond/ListedForcesTest -25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 -25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 -25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 -25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 -25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 -25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 -25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 -25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 -25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 -25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 -25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 -25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 -25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 -25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 -25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 -25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 -25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 -25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 -25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 -25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 -25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 -25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 -25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 -25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) -25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 -25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) -25: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) -25: -25: [----------] 33 tests from Angle/ListedForcesTest -25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 -25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 -25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 -25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 -25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 -25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 -25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 -25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 -25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 -25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 -25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 -25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 -25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 -25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 -25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 -25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 -25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 -25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 -25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 -25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 -25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 -25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 -25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 -25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 -25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 -25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 -25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 -25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 -25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 -25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 -25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 -25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 -25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) -25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 -25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) -25: [----------] 33 tests from Angle/ListedForcesTest (4 ms total) -25: -25: [----------] 18 tests from Dihedral/ListedForcesTest -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 -25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) -25: [----------] 18 tests from Dihedral/ListedForcesTest (3 ms total) -25: -25: [----------] 12 tests from Polarize/ListedForcesTest -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 -25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) -25: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) -25: -25: [----------] 18 tests from Restraints/ListedForcesTest -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) -25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 -25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) -25: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) -25: -25: [----------] 3 tests from BondZeroLength/ListedForcesTest -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 -25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) -25: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) -25: -25: [----------] 3 tests from AngleZero/ListedForcesTest -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) -25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 -25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) -25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) -25: -25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) -25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 -25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) -25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) -25: -25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) -25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 -25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) -25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) -25: -25: [----------] Global test environment tear-down -25: [==========] 132 tests from 9 test suites ran. (18 ms total) -25: [ PASSED ] 132 tests. -25/92 Test #25: ListedForcesTest .......................... Passed 0.04 sec -test 26 - Start 26: NbnxmTests - -26: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbnxmTests.xml" -26: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests -26: Test timeout computed to be: 30 -26: [==========] Running 383 tests from 4 test suites. -26: [----------] Global test environment set-up. -26: [----------] 18 tests from KernelSetupTest -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF -26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut -26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable -26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin -26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald -26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) -26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin -26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom -26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone -26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch -26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) -26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows -26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) -26: [----------] 18 tests from KernelSetupTest (0 ms total) -26: -26: [----------] 2 tests from SimdEnergyAccumulatorTest -26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM -26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) -26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM -26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) -26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) -26: -26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) -26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 -26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) -26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) -26: -26: [----------] 360 tests from Combinations/NbnxmKernelTest -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (5 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -26: Analytical Ewald is not implemented for the plain-C kernel, skip this test -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -26: There are no combination rule versions of the plain-C kernel -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -26: Cannot test or generate data for 2xNN kernels without suitable SIMD support -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -26: [----------] 360 tests from Combinations/NbnxmKernelTest (414 ms total) -26: -26: [----------] Global test environment tear-down -26: [==========] 383 tests from 4 test suites ran. (415 ms total) -26: [ PASSED ] 185 tests. -26: [ SKIPPED ] 198 tests, listed below: -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -26/92 Test #26: NbnxmTests ................................ Passed 0.48 sec -test 27 - Start 27: NbnxmGpuTests - -27: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" -27: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/nbnxm/tests -27: Test timeout computed to be: 30 -27: [==========] Running 0 tests from 0 test suites. -27: [==========] 0 tests from 0 test suites ran. (0 ms total) -27: [ PASSED ] 0 tests. -27/92 Test #27: NbnxmGpuTests ............................. Passed 0.03 sec -test 28 - Start 28: CommandLineUnitTests - -28: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" -28: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests -28: Test timeout computed to be: 30 -28: [==========] Running 60 tests from 7 test suites. -28: [----------] Global test environment set-up. -28: [----------] 3 tests from CommandLineHelpModuleTest -28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp -28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) -28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic -28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) -28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp -28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) -28: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) -28: -28: [----------] 7 tests from CommandLineHelpWriterTest -28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes -28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables -28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions -28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions -28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups -28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText -28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) -28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues -28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) -28: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) -28: -28: [----------] 6 tests from CommandLineModuleManagerTest -28: [ RUN ] CommandLineModuleManagerTest.RunsModule -28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule -28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) -28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames -28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) -28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) -28: -28: [----------] 13 tests from CommandLineParserTest -28: [ RUN ] CommandLineParserTest.HandlesSingleValues -28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument -28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument -28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) -28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument -28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers -28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesString -28: [ OK ] CommandLineParserTest.HandlesString (0 ms) -28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues -28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix -28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers -28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) -28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown -28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) -28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault -28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) -28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments -28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) -28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions -28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) -28: [----------] 13 tests from CommandLineParserTest (0 ms total) -28: -28: [----------] 6 tests from CommandLineProgramContextTest -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) -28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink -28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) -28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) -28: -28: [----------] 3 tests from OutputNamesTest -28: [ RUN ] OutputNamesTest.CanBeSuffixed -28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) -28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend -28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) -28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded -28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) -28: [----------] 3 tests from OutputNamesTest (0 ms total) -28: -28: [----------] 22 tests from ParseCommonArgsTest -28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs -28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args -28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs -28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs -28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs -28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum -28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs -28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs -28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit -28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs -28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs -28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults -28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName -28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) -28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension -28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles -28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles -28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) -28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified -28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) -28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles -28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) -28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension -28: Value is /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo -28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) -28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile -28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) -28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName -28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (9 ms) -28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs -28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) -28: [----------] 22 tests from ParseCommonArgsTest (11 ms total) -28: -28: [----------] Global test environment tear-down -28: [==========] 60 tests from 7 test suites ran. (14 ms total) -28: [ PASSED ] 60 tests. -28/92 Test #28: CommandLineUnitTests ...................... Passed 0.03 sec -test 29 - Start 29: DomDecTests - -29: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/DomDecTests.xml" -29: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/domdec/tests -29: Test timeout computed to be: 30 -29: [==========] Running 9 tests from 2 test suites. -29: [----------] Global test environment set-up. -29: [----------] 7 tests from HashedMap -29: [ RUN ] HashedMap.InsertsFinds -29: [ OK ] HashedMap.InsertsFinds (0 ms) -29: [ RUN ] HashedMap.NegativeKeysWork -29: [ OK ] HashedMap.NegativeKeysWork (0 ms) -29: [ RUN ] HashedMap.InsertsErases -29: [ OK ] HashedMap.InsertsErases (0 ms) -29: [ RUN ] HashedMap.InsertsOrAssigns -29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) -29: [ RUN ] HashedMap.Clears -29: [ OK ] HashedMap.Clears (0 ms) -29: [ RUN ] HashedMap.LinkedEntries -29: [ OK ] HashedMap.LinkedEntries (0 ms) -29: [ RUN ] HashedMap.ResizesTable -29: [ OK ] HashedMap.ResizesTable (0 ms) -29: [----------] 7 tests from HashedMap (0 ms total) -29: -29: [----------] 2 tests from LocalAtomSetManager -29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet -29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) -29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices -29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) -29: [----------] 2 tests from LocalAtomSetManager (0 ms total) -29: -29: [----------] Global test environment tear-down -29: [==========] 9 tests from 2 test suites ran. (0 ms total) -29: [ PASSED ] 9 tests. -29/92 Test #29: DomDecTests ............................... Passed 0.01 sec -test 30 - Start 30: DomDecMpiTests - -30: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" -30: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/domdec/tests -30: Test timeout computed to be: 30 -30: [==========] Running 4 tests from 1 test suite. -30: [----------] Global test environment set-up. -30: [----------] 4 tests from HaloExchangeTest -30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse -30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses -30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim -30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) -30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 -30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) -30: [----------] 4 tests from HaloExchangeTest (1 ms total) -30: -30: [----------] Global test environment tear-down -30: [==========] 4 tests from 1 test suite ran. (1 ms total) -30: [ PASSED ] 4 tests. -30/92 Test #30: DomDecMpiTests ............................ Passed 0.03 sec -test 31 - Start 31: EwaldUnitTests - -31: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" -31: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/ewald/tests -31: Test timeout computed to be: 30 -31: [==========] Running 407 tests from 9 test suites. -31: [----------] Global test environment set-up. -31: [----------] 6 tests from SeparatePmeRanksPermittedTest -31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons -31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled -31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag -31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) -31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText -31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) -31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) -31: -31: [----------] 108 tests from Pme_SplineAndSpreadTest -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) -31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) -31: [----------] 108 tests from Pme_SplineAndSpreadTest (90 ms total) -31: -31: [----------] 64 tests from Pme_SolveTest -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [----------] 64 tests from Pme_SolveTest (15 ms total) -31: -31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (5 ms total) -31: -31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (8 ms total) -31: -31: [----------] 64 tests from PmeDiffEps_SolveTest -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -31: Test is being skipped because: -31: CPU PME solve does not implement XYZ grid ordering -31: -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -31: [----------] 64 tests from PmeDiffEps_SolveTest (14 ms total) -31: -31: [----------] 72 tests from Pme_GatherTest -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -31: [----------] 72 tests from Pme_GatherTest (19 ms total) -31: -31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) -31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 -31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) -31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (2 ms total) -31: -31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) -31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 -31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) -31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (74 ms total) -31: -31: [----------] Global test environment tear-down -31: [==========] 407 tests from 9 test suites ran. (232 ms total) -31: [ PASSED ] 311 tests. -31: [ SKIPPED ] 96 tests, listed below: -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -31/92 Test #31: EwaldUnitTests ............................ Passed 0.27 sec -test 32 - Start 32: FFTUnitTests - -32: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" -32: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/fft/tests -32: Test timeout computed to be: 1920 -32: [==========] Running 15 tests from 4 test suites. -32: [----------] Global test environment set-up. -32: [----------] 2 tests from ManyFFTTest -32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test -32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) -32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test -32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (11 ms) -32: [----------] 2 tests from ManyFFTTest (17 ms total) -32: -32: [----------] 1 test from FFTTest -32: [ RUN ] FFTTest.Real2DLength18_15Test -32: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) -32: [----------] 1 test from FFTTest (3 ms total) -32: -32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) -32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 -32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms) -32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (24 ms total) -32: -32: [----------] 2 tests from Works/ParameterizedFFTTest3D -32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 -32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) -32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 -32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) -32: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) -32: -32: [----------] Global test environment tear-down -32: [==========] 15 tests from 4 test suites ran. (48 ms total) -32: [ PASSED ] 15 tests. -32/92 Test #32: FFTUnitTests .............................. Passed 0.16 sec -test 33 - Start 33: GpuUtilsUnitTests - -33: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" -33: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gpu_utils/tests -33: Test timeout computed to be: 30 -33: [==========] Running 67 tests from 22 test suites. -33: [----------] Global test environment set-up. -33: [----------] 2 tests from ClfftInitializer -33: [ RUN ] ClfftInitializer.SingleInitializationWorks -33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) -33: [ RUN ] ClfftInitializer.TwoInitializationsWork -33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) -33: [----------] 2 tests from ClfftInitializer (0 ms total) -33: -33: [----------] 1 test from DevicesAvailable -33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice -33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) -33: [----------] 1 test from DevicesAvailable (0 ms total) -33: -33: [----------] 1 test from DeviceStreamManagerTest -33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice -33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) -33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int -33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double -33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) -33: -33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly -33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks -33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory -33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) -33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double -33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks -33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork -33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) -33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve -33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) -33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector -33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.Swap -33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/0.Comparison -33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double -33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector -33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.Swap -33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/1.Comparison -33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector -33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.Swap -33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/2.Comparison -33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) -33: -33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly -33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector -33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment -33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction -33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.Swap -33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) -33: [ RUN ] HostAllocatorTestNoMem/3.Comparison -33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) -33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) -33: -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) -33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) -33: -33: [----------] 1 test from HostAllocatorUntypedTest -33: [ RUN ] HostAllocatorUntypedTest.Comparison -33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) -33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/0.Move -33: [ OK ] AllocatorTest/0.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/0 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/1.Move -33: [ OK ] AllocatorTest/1.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/1 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> -33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/2.Move -33: [ OK ] AllocatorTest/2.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/2 (0 ms total) -33: -33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -33: [ RUN ] AllocatorTest/3.Move -33: [ OK ] AllocatorTest/3.Move (0 ms) -33: [----------] 4 tests from AllocatorTest/3 (0 ms total) -33: -33: [----------] Global test environment tear-down -33: [==========] 67 tests from 22 test suites ran. (1 ms total) -33: [ PASSED ] 67 tests. -33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.05 sec -test 34 - Start 34: HardwareUnitTests - -34: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" -34: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/hardware/tests -34: Test timeout computed to be: 30 -34: [==========] Running 22 tests from 10 test suites. -34: [----------] Global test environment set-up. -34: [----------] 1 test from CpuInfoTest -34: [ RUN ] CpuInfoTest.SupportLevel -34: [ OK ] CpuInfoTest.SupportLevel (2 ms) -34: [----------] 1 test from CpuInfoTest (2 ms total) -34: -34: [----------] 4 tests from HardwareTopologyTest -34: [ RUN ] HardwareTopologyTest.Execute -34: [ OK ] HardwareTopologyTest.Execute (17 ms) -34: [ RUN ] HardwareTopologyTest.HwlocExecute -34: [ OK ] HardwareTopologyTest.HwlocExecute (22 ms) -34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency -34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (15 ms) -34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency -34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (14 ms) -34: [----------] 4 tests from HardwareTopologyTest (69 ms total) -34: -34: [----------] 1 test from DevicesManagerTest -34: [ RUN ] DevicesManagerTest.Serialization -34: [ OK ] DevicesManagerTest.Serialization (0 ms) -34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid -34: [----------] 1 test from DevicesManagerTest (0 ms total) -34: -34: [----------] 1 test from UuidStringTest -34: [ RUN ] UuidStringTest.Works -34: [ OK ] UuidStringTest.Works (0 ms) -34: [----------] 1 test from UuidStringTest (0 ms total) -34: -34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 -34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) -34: -34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 -34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) -34: -34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest -34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 -34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 -34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) -34: -34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest -34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) -34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) -34: -34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest -34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) -34: -34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest -34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (1 ms total) -34: -34: [----------] Global test environment tear-down -34: [==========] 22 tests from 10 test suites ran. (83 ms total) -34: [ PASSED ] 22 tests. -34: -34: YOU HAVE 1 DISABLED TEST -34: -34/92 Test #34: HardwareUnitTests ......................... Passed 0.11 sec -test 35 - Start 35: MathUnitTests - -35: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MathUnitTests.xml" -35: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/math/tests -35: Test timeout computed to be: 30 -35: [==========] Running 328 tests from 41 test suites. -35: [----------] Global test environment set-up. -35: [----------] 1 test from EmptyArrayRefWithPaddingTest -35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty -35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) -35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) -35: -35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest -35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty -35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) -35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) -35: -35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding -35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks -35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) -35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks -35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) -35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) -35: -35: [----------] 2 tests from InvertBoxMatrixTest -35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent -35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) -35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace -35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) -35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) -35: -35: [----------] 8 tests from ComplexNumberTest -35: [ RUN ] ComplexNumberTest.RealComplexMultiply -35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) -35: [ RUN ] ComplexNumberTest.RealComplexExp -35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexAdd -35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexSubtract -35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexMultiply -35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexDivision -35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexConjugate -35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) -35: [ RUN ] ComplexNumberTest.ComplexAbs2 -35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) -35: [----------] 8 tests from ComplexNumberTest (0 ms total) -35: -35: [----------] 11 tests from TranslateAndScaleTest -35: [ RUN ] TranslateAndScaleTest.identityTransformation -35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling -35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation -35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial -35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) -35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector -35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingIdentity -35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial -35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector -35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero -35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero -35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) -35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector -35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) -35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) -35: -35: [----------] 3 tests from AffineTransformationTest -35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors -35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) -35: [ RUN ] AffineTransformationTest.applyTransformationToVectors -35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) -35: [ RUN ] AffineTransformationTest.retrieveGradient -35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) -35: [----------] 3 tests from AffineTransformationTest (0 ms total) -35: -35: [----------] 14 tests from DensitySimilarityTest -35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect -35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect -35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch -35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) -35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch -35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) -35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect -35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero -35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect -35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect -35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne -35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (17 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated -35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (14 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated -35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) -35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect -35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.NormalizationCorrect -35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) -35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive -35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) -35: [----------] 14 tests from DensitySimilarityTest (33 ms total) -35: -35: [----------] 6 tests from StructureSimilarityTest -35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD -35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) -35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho -35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD -35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho -35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex -35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) -35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex -35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) -35: [----------] 6 tests from StructureSimilarityTest (0 ms total) -35: -35: [----------] 8 tests from ExponentialMovingAverage -35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero -35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) -35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative -35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) -35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue -35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) -35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue -35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) -35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly -35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) -35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing -35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) -35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect -35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) -35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree -35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) -35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) -35: -35: [----------] 21 tests from FunctionTest -35: [ RUN ] FunctionTest.StaticLog2 -35: [ OK ] FunctionTest.StaticLog2 (0 ms) -35: [ RUN ] FunctionTest.Log2I32Bit -35: [ OK ] FunctionTest.Log2I32Bit (0 ms) -35: [ RUN ] FunctionTest.Log2I64Bit -35: [ OK ] FunctionTest.Log2I64Bit (0 ms) -35: [ RUN ] FunctionTest.GreatestCommonDivisor -35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) -35: [ RUN ] FunctionTest.InvsqrtFloat -35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) -35: [ RUN ] FunctionTest.InvsqrtDouble -35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) -35: [ RUN ] FunctionTest.InvsqrtInteger -35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) -35: [ RUN ] FunctionTest.InvcbrtFloat -35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) -35: [ RUN ] FunctionTest.InvcbrtDouble -35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) -35: [ RUN ] FunctionTest.InvcbrtInteger -35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) -35: [ RUN ] FunctionTest.SixthrootFloat -35: [ OK ] FunctionTest.SixthrootFloat (0 ms) -35: [ RUN ] FunctionTest.SixthrootDouble -35: [ OK ] FunctionTest.SixthrootDouble (0 ms) -35: [ RUN ] FunctionTest.SixthrootInteger -35: [ OK ] FunctionTest.SixthrootInteger (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootFloat -35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootDouble -35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) -35: [ RUN ] FunctionTest.InvsixthrootInteger -35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) -35: [ RUN ] FunctionTest.Powers -35: [ OK ] FunctionTest.Powers (0 ms) -35: [ RUN ] FunctionTest.ErfInvFloat -35: [ OK ] FunctionTest.ErfInvFloat (0 ms) -35: [ RUN ] FunctionTest.ErfInvDouble -35: [ OK ] FunctionTest.ErfInvDouble (0 ms) -35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat -35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) -35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble -35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) -35: [----------] 21 tests from FunctionTest (1 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char -35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char -35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short -35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short -35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int -35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int -35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long -35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) -35: -35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long -35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo -35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) -35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp -35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) -35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) -35: -35: [----------] 4 tests from GaussianOn1DLattice -35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne -35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) -35: [ RUN ] GaussianOn1DLattice.isCorrect -35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) -35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero -35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) -35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange -35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) -35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) -35: -35: [----------] 9 tests from GaussTransformTest -35: [ RUN ] GaussTransformTest.isZeroUponConstruction -35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) -35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss -35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) -35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero -35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) -35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ -35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) -35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero -35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) -35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues -35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) -35: [ RUN ] GaussTransformTest.view -35: [ OK ] GaussTransformTest.view (0 ms) -35: [----------] 9 tests from GaussTransformTest (0 ms total) -35: -35: [----------] 3 tests from DensityFittingForce -35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity -35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) -35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections -35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) -35: [ RUN ] DensityFittingForce.pullsTowardsDerivative -35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) -35: [----------] 3 tests from DensityFittingForce (0 ms total) -35: -35: [----------] 2 tests from InvertMatrixTest -35: [ RUN ] InvertMatrixTest.IdentityIsImpotent -35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) -35: [ RUN ] InvertMatrixTest.ComputesInverse -35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) -35: [----------] 2 tests from InvertMatrixTest (0 ms total) -35: -35: [----------] 22 tests from MatrixTest -35: [ RUN ] MatrixTest.canSetFromArray -35: [ OK ] MatrixTest.canSetFromArray (0 ms) -35: [ RUN ] MatrixTest.canSetStaticallyFromList -35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) -35: [ RUN ] MatrixTest.canConstructAndFill -35: [ OK ] MatrixTest.canConstructAndFill (0 ms) -35: [ RUN ] MatrixTest.canSetValues -35: [ OK ] MatrixTest.canSetValues (0 ms) -35: [ RUN ] MatrixTest.canCopyAssign -35: [ OK ] MatrixTest.canCopyAssign (0 ms) -35: [ RUN ] MatrixTest.canSwap -35: [ OK ] MatrixTest.canSwap (0 ms) -35: [ RUN ] MatrixTest.staticMultiDimArrayExtent -35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) -35: [ RUN ] MatrixTest.canAddMatrix -35: [ OK ] MatrixTest.canAddMatrix (0 ms) -35: [ RUN ] MatrixTest.canSubstractMatrix -35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) -35: [ RUN ] MatrixTest.canNegateMatrix -35: [ OK ] MatrixTest.canNegateMatrix (0 ms) -35: [ RUN ] MatrixTest.determinantWorks -35: [ OK ] MatrixTest.determinantWorks (0 ms) -35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero -35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) -35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix -35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) -35: [ RUN ] MatrixTest.traceWorks -35: [ OK ] MatrixTest.traceWorks (0 ms) -35: [ RUN ] MatrixTest.transposeWorks -35: [ OK ] MatrixTest.transposeWorks (0 ms) -35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix -35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) -35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix -35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) -35: [ RUN ] MatrixTest.canFillLegacyMatrix -35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) -35: [ RUN ] MatrixTest.IdentityMatrix -35: [ OK ] MatrixTest.IdentityMatrix (0 ms) -35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct -35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) -35: [ RUN ] MatrixTest.MatrixMatrixMultiplication -35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) -35: [ RUN ] MatrixTest.MatrixVectorMultiplication -35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) -35: [----------] 22 tests from MatrixTest (0 ms total) -35: -35: [----------] 25 tests from MultiDimArrayTest -35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic -35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic -35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic -35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic -35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic -35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic -35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic -35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic -35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic -35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic -35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic -35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic -35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSwapStatic -35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) -35: [ RUN ] MultiDimArrayTest.canSwapDynamic -35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) -35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent -35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) -35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue -35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) -35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray -35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) -35: [ RUN ] MultiDimArrayTest.conversionToView -35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) -35: [ RUN ] MultiDimArrayTest.conversionToConstView -35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) -35: [ RUN ] MultiDimArrayTest.viewBegin -35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) -35: [ RUN ] MultiDimArrayTest.viewEnd -35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) -35: [ RUN ] MultiDimArrayTest.constViewConstBegin -35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) -35: [ RUN ] MultiDimArrayTest.constViewConstEnd -35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) -35: [----------] 25 tests from MultiDimArrayTest (0 ms total) -35: -35: [----------] 4 tests from MultiDimArrayToMdSpanTest -35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) -35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan -35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) -35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) -35: -35: [----------] 9 tests from NelderMeadSimplexTest -35: [ RUN ] NelderMeadSimplexTest.BestVertex -35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) -35: [ RUN ] NelderMeadSimplexTest.WorstVertex -35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) -35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue -35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) -35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint -35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint -35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint -35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) -35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst -35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) -35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest -35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) -35: [ RUN ] NelderMeadSimplexTest.OrientedLength -35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) -35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) -35: -35: [----------] 2 tests from NelderMead -35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly -35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) -35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly -35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) -35: [----------] 2 tests from NelderMead (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ResizeWorks -35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ReserveWorks -35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanCopyAssign -35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanMoveAssign -35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/0.CanSwap -35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ResizeWorks -35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ReserveWorks -35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanCopyAssign -35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanMoveAssign -35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/1.CanSwap -35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator -35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ResizeWorks -35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ReserveWorks -35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanCopyAssign -35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanMoveAssign -35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/2.CanSwap -35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > -35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ResizeWorks -35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ReserveWorks -35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanCopyAssign -35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanMoveAssign -35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/3.CanSwap -35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > -35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ResizeWorks -35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ReserveWorks -35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanCopyAssign -35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanMoveAssign -35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/4.CanSwap -35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ResizeWorks -35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ReserveWorks -35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanCopyAssign -35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanMoveAssign -35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/5.CanSwap -35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ResizeWorks -35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ReserveWorks -35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanCopyAssign -35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanMoveAssign -35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/6.CanSwap -35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator -35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ResizeWorks -35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ReserveWorks -35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanCopyAssign -35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanMoveAssign -35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/7.CanSwap -35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ResizeWorks -35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ReserveWorks -35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanCopyAssign -35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanMoveAssign -35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/8.CanSwap -35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) -35: -35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks -35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ResizeWorks -35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ReserveWorks -35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve -35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks -35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks -35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks -35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) -35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical -35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanCopyAssign -35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanMoveAssign -35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) -35: [ RUN ] PaddedVectorTest/9.CanSwap -35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) -35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) -35: -35: [----------] 41 tests from RVecTest -35: [ RUN ] RVecTest.CanBeStoredInVector -35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) -35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec -35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) -35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec -35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) -35: [ RUN ] RVecTest.WorksAsMutable_rvec -35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) -35: [ RUN ] RVecTest.WorksAs_rvec_Array -35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) -35: [ RUN ] RVecTest.ComparesEqual -35: [ OK ] RVecTest.ComparesEqual (0 ms) -35: [ RUN ] RVecTest.ComparesUnequal -35: [ OK ] RVecTest.ComparesUnequal (0 ms) -35: [ RUN ] RVecTest.CanAddRVecToRvec -35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) -35: [ RUN ] RVecTest.CanAddAssignRVecToRvec -35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) -35: [ RUN ] RVecTest.CanSubtractRVecFromRvec -35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) -35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec -35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) -35: [ RUN ] RVecTest.CanDotProductRVecByRvec -35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) -35: [ RUN ] RVecTest.CanCrossProductRVecByRvec -35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) -35: [ RUN ] RVecTest.CanDivideRVecInplace -35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) -35: [ RUN ] RVecTest.CanScaleRVec -35: [ OK ] RVecTest.CanScaleRVec (0 ms) -35: [ RUN ] RVecTest.CanDivideRVec -35: [ OK ] RVecTest.CanDivideRVec (0 ms) -35: [ RUN ] RVecTest.CanDoUnitvFromRVec -35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) -35: [ RUN ] RVecTest.CanSqLengthOfRVec -35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanLengthOfRVec -35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanCastToRVec -35: [ OK ] RVecTest.CanCastToRVec (0 ms) -35: [ RUN ] RVecTest.CanCastToDVec -35: [ OK ] RVecTest.CanCastToDVec (0 ms) -35: [ RUN ] RVecTest.CanLeftScalarMultiply -35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) -35: [ RUN ] RVecTest.CanRightScalarMultiply -35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) -35: [ RUN ] RVecTest.CanGetUnitvFromRVec -35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) -35: [ RUN ] RVecTest.CanGetSqLengthOfRVec -35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanGetLengthOfRVec -35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) -35: [ RUN ] RVecTest.CanDoCrossProductOfRVec -35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) -35: [ RUN ] RVecTest.CanDoDotProductOfRVec -35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) -35: [ RUN ] RVecTest.CanScaleByVector -35: [ OK ] RVecTest.CanScaleByVector (0 ms) -35: [ RUN ] RVecTest.CanNegate -35: [ OK ] RVecTest.CanNegate (0 ms) -35: [ RUN ] RVecTest.asIVec -35: [ OK ] RVecTest.asIVec (0 ms) -35: [ RUN ] RVecTest.elementWiseMin -35: [ OK ] RVecTest.elementWiseMin (0 ms) -35: [ RUN ] RVecTest.elementWiseMax -35: [ OK ] RVecTest.elementWiseMax (0 ms) -35: [ RUN ] RVecTest.WorksAs_dvec_Reference -35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) -35: [ RUN ] RVecTest.WorksAs_ivec_Reference -35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) -35: [ RUN ] RVecTest.WorksAs_rvec_Reference -35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) -35: [ RUN ] RVecTest.CopyConstructorWorks -35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) -35: [ RUN ] RVecTest.CopyAssignmentWorks -35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) -35: [ RUN ] RVecTest.MoveConstructorWorks -35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) -35: [ RUN ] RVecTest.MoveAssignmentWorks -35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) -35: [ RUN ] RVecTest.UsableInConstexpr -35: [ OK ] RVecTest.UsableInConstexpr (0 ms) -35: [----------] 41 tests from RVecTest (0 ms total) -35: -35: [----------] Global test environment tear-down -35: [==========] 328 tests from 41 test suites ran. (36 ms total) -35: [ PASSED ] 328 tests. -35/92 Test #35: MathUnitTests ............................. Passed 0.13 sec -test 36 - Start 36: MdrunUtilityUnitTests - -36: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" -36: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests -36: Test timeout computed to be: 30 -36: [==========] Running 21 tests from 2 test suites. -36: [----------] Global test environment set-up. -36: [----------] 4 tests from MDModulesNotifierTest -36: [ RUN ] MDModulesNotifierTest.AddConsumer -36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter -36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers -36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) -36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources -36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) -36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) -36: -36: [----------] 17 tests from ThreadAffinityTest -36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled -36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported -36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware -36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) -36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride -36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced -36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread -36: NOTE: Affinity setting failed. -36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto -36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced -36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) -36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads -36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) -36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing -36: NOTE: Affinity setting for 1/2 threads failed. -36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) -36: [----------] 17 tests from ThreadAffinityTest (2 ms total) -36: -36: [----------] Global test environment tear-down -36: [==========] 21 tests from 2 test suites ran. (3 ms total) -36: [ PASSED ] 21 tests. -36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.01 sec -test 37 - Start 37: MdrunUtilityMpiUnitTests - -37: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" -37: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdrunutility/tests -37: Test timeout computed to be: 30 -37: [==========] Running 13 tests from 2 test suites. -37: [----------] Global test environment set-up. -37: [----------] 6 tests from ThreadAffinityMultiRankTest -37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode -37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride -37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes -37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled -37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto -37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) -37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce -37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (20 ms) -37: [----------] 6 tests from ThreadAffinityMultiRankTest (24 ms total) -37: -37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) -37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly -37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) -37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (5 ms total) -37: -37: [----------] Global test environment tear-down -37: [==========] 13 tests from 2 test suites ran. (30 ms total) -37: [ PASSED ] 13 tests. -37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 0.04 sec -test 38 - Start 38: MDSpanTests - -38: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MDSpanTests.xml" -38: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdspan/tests -38: Test timeout computed to be: 30 -38: [==========] Running 32 tests from 7 test suites. -38: [----------] Global test environment set-up. -38: [----------] 4 tests from BasicAccessorPolicy -38: [ RUN ] BasicAccessorPolicy.Decay -38: [ OK ] BasicAccessorPolicy.Decay (0 ms) -38: [ RUN ] BasicAccessorPolicy.Access -38: [ OK ] BasicAccessorPolicy.Access (0 ms) -38: [ RUN ] BasicAccessorPolicy.Offset -38: [ OK ] BasicAccessorPolicy.Offset (0 ms) -38: [ RUN ] BasicAccessorPolicy.CopyAccessor -38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) -38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) -38: -38: [----------] 4 tests from ExtentsTest -38: [ RUN ] ExtentsTest.Construction -38: [ OK ] ExtentsTest.Construction (0 ms) -38: [ RUN ] ExtentsTest.PurelyStatic -38: [ OK ] ExtentsTest.PurelyStatic (0 ms) -38: [ RUN ] ExtentsTest.RankNought -38: [ OK ] ExtentsTest.RankNought (0 ms) -38: [ RUN ] ExtentsTest.Assignment -38: [ OK ] ExtentsTest.Assignment (0 ms) -38: [----------] 4 tests from ExtentsTest (0 ms total) -38: -38: [----------] 8 tests from MdSpanExtension -38: [ RUN ] MdSpanExtension.SlicingAllStatic -38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) -38: [ RUN ] MdSpanExtension.SlicingDynamic -38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) -38: [ RUN ] MdSpanExtension.SlicingAllStatic3D -38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) -38: [ RUN ] MdSpanExtension.SlicingEqualsView3D -38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) -38: [ RUN ] MdSpanExtension.additionWorks -38: [ OK ] MdSpanExtension.additionWorks (0 ms) -38: [ RUN ] MdSpanExtension.subtractionWorks -38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) -38: [ RUN ] MdSpanExtension.multiplicationWorks -38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) -38: [ RUN ] MdSpanExtension.divisionWorks -38: [ OK ] MdSpanExtension.divisionWorks (0 ms) -38: [----------] 8 tests from MdSpanExtension (0 ms total) -38: -38: [----------] 3 tests from LayoutTests -38: [ RUN ] LayoutTests.LayoutRightConstruction -38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) -38: [ RUN ] LayoutTests.LayoutRightProperties -38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) -38: [ RUN ] LayoutTests.LayoutRightOperator -38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) -38: [----------] 3 tests from LayoutTests (0 ms total) -38: -38: [----------] 1 test from MdSpanTest -38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly -38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) -38: [----------] 1 test from MdSpanTest (0 ms total) -38: -38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -38: [ RUN ] MdSpanTest/0.Rank -38: [ OK ] MdSpanTest/0.Rank (0 ms) -38: [ RUN ] MdSpanTest/0.DynamicRank -38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) -38: [ RUN ] MdSpanTest/0.Extents -38: [ OK ] MdSpanTest/0.Extents (0 ms) -38: [ RUN ] MdSpanTest/0.Strides -38: [ OK ] MdSpanTest/0.Strides (0 ms) -38: [ RUN ] MdSpanTest/0.Properties -38: [ OK ] MdSpanTest/0.Properties (0 ms) -38: [ RUN ] MdSpanTest/0.Operator -38: [ OK ] MdSpanTest/0.Operator (0 ms) -38: [----------] 6 tests from MdSpanTest/0 (0 ms total) -38: -38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -38: [ RUN ] MdSpanTest/1.Rank -38: [ OK ] MdSpanTest/1.Rank (0 ms) -38: [ RUN ] MdSpanTest/1.DynamicRank -38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) -38: [ RUN ] MdSpanTest/1.Extents -38: [ OK ] MdSpanTest/1.Extents (0 ms) -38: [ RUN ] MdSpanTest/1.Strides -38: [ OK ] MdSpanTest/1.Strides (0 ms) -38: [ RUN ] MdSpanTest/1.Properties -38: [ OK ] MdSpanTest/1.Properties (0 ms) -38: [ RUN ] MdSpanTest/1.Operator -38: [ OK ] MdSpanTest/1.Operator (0 ms) -38: [----------] 6 tests from MdSpanTest/1 (0 ms total) -38: -38: [----------] Global test environment tear-down -38: [==========] 32 tests from 7 test suites ran. (0 ms total) -38: [ PASSED ] 32 tests. -38/92 Test #38: MDSpanTests ............................... Passed 0.01 sec -test 39 - Start 39: MdtypesUnitTest - -39: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" -39: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/mdtypes/tests -39: Test timeout computed to be: 30 -39: [==========] Running 97 tests from 7 test suites. -39: [----------] Global test environment set-up. -39: [----------] 4 tests from ForeingLambdaTermsDhdl -39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks -39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear -39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative -39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) -39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul -39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) -39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) -39: -39: [----------] 4 tests from ObservablesReducerTest -39: [ RUN ] ObservablesReducerTest.CanMoveAssign -39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) -39: [ RUN ] ObservablesReducerTest.CanMoveConstruct -39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) -39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers -39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) -39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber -39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) -39: [----------] 4 tests from ObservablesReducerTest (0 ms total) -39: -39: [----------] 2 tests from CheckpointDataTest -39: [ RUN ] CheckpointDataTest.SingleDataTest -39: [ OK ] CheckpointDataTest.SingleDataTest (1415 ms) -39: [ RUN ] CheckpointDataTest.MultiDataTest -39: [ OK ] CheckpointDataTest.MultiDataTest (11416 ms) -39: [----------] 2 tests from CheckpointDataTest (12831 ms total) -39: -39: [----------] 7 tests from ForceBuffers -39: [ RUN ] ForceBuffers.ConstructsUnpinned -39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) -39: [ RUN ] ForceBuffers.ConstructsPinned -39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) -39: [ RUN ] ForceBuffers.ConstructsEmpty -39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) -39: [ RUN ] ForceBuffers.ResizeWorks -39: [ OK ] ForceBuffers.ResizeWorks (0 ms) -39: [ RUN ] ForceBuffers.PaddingWorks -39: [ OK ] ForceBuffers.PaddingWorks (0 ms) -39: [ RUN ] ForceBuffers.CopyWorks -39: [ OK ] ForceBuffers.CopyWorks (0 ms) -39: [ RUN ] ForceBuffers.CopyDoesNotPin -39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) -39: [----------] 7 tests from ForceBuffers (0 ms total) -39: -39: [----------] 5 tests from MultipleTimeStepping -39: [ RUN ] MultipleTimeStepping.ChecksNumLevels -39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) -39: [ RUN ] MultipleTimeStepping.SelectsForceGroups -39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksStepFactor -39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel -39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) -39: [ RUN ] MultipleTimeStepping.ChecksIntegrator -39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) -39: [----------] 5 tests from MultipleTimeStepping (0 ms total) -39: -39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) -39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 -39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) -39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) -39: -39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) -39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 -39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) -39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) -39: -39: [----------] Global test environment tear-down -39: [==========] 97 tests from 7 test suites ran. (12833 ms total) -39: [ PASSED ] 97 tests. -39/92 Test #39: MdtypesUnitTest ........................... Passed 12.84 sec -test 40 - Start 40: OnlineHelpUnitTests - -40: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" -40: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/onlinehelp/tests -40: Test timeout computed to be: 30 -40: [==========] Running 22 tests from 4 test suites. -40: [----------] Global test environment set-up. -40: [----------] 6 tests from TextTableFormatterTest -40: [ RUN ] TextTableFormatterTest.HandlesBasicCase -40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles -40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesIndentation -40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines -40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding -40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) -40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns -40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) -40: [----------] 6 tests from TextTableFormatterTest (0 ms total) -40: -40: [----------] 3 tests from HelpManagerTest -40: [ RUN ] HelpManagerTest.HandlesRootTopic -40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) -40: [ RUN ] HelpManagerTest.HandlesSubTopics -40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) -40: [ RUN ] HelpManagerTest.HandlesInvalidTopics -40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) -40: [----------] 3 tests from HelpManagerTest (0 ms total) -40: -40: [----------] 2 tests from HelpTopicFormattingTest -40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic -40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) -40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics -40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) -40: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) -40: -40: [----------] 11 tests from HelpWriterContextTest -40: [ RUN ] HelpWriterContextTest.FormatsParagraphs -40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs -40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) -40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace -40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralText -40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning -40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation -40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsBulletList -40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList -40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable -40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsGridTable -40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) -40: [ RUN ] HelpWriterContextTest.FormatsTitles -40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) -40: [----------] 11 tests from HelpWriterContextTest (0 ms total) -40: -40: [----------] Global test environment tear-down -40: [==========] 22 tests from 4 test suites ran. (2 ms total) -40: [ PASSED ] 22 tests. -40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.01 sec -test 41 - Start 41: OptionsUnitTests - -41: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" -41: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/options/tests -41: Test timeout computed to be: 30 -41: [==========] Running 112 tests from 18 test suites. -41: [----------] Global test environment set-up. -41: [----------] 5 tests from AbstractOptionStorageTest -41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish -41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval -41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition -41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) -41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition -41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) -41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues -41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) -41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) -41: -41: [----------] 10 tests from FileNameOptionTest -41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue -41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption -41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension -41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix -41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) -41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix -41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension -41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) -41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue -41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) -41: [----------] 10 tests from FileNameOptionTest (0 ms total) -41: -41: [----------] 16 tests from FileNameOptionManagerTest -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension -41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile -41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified -41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile -41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) -41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking -41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) -41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile -41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) -41: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) -41: -41: [----------] 1 test from OptionsTest -41: [ RUN ] OptionsTest.FailsOnNonsafeStorage -41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) -41: [----------] 1 test from OptionsTest (0 ms total) -41: -41: [----------] 9 tests from OptionsAssignerTest -41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter -41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue -41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter -41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter -41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMissingValue -41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesExtraValue -41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesGroups -41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesSections -41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) -41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources -41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) -41: [----------] 9 tests from OptionsAssignerTest (0 ms total) -41: -41: [----------] 4 tests from OptionsAssignerBooleanTest -41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue -41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue -41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo -41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) -41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue -41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) -41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) -41: -41: [----------] 13 tests from OptionsAssignerIntegerTest -41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue -41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow -41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue -41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet -41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet -41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues -41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector -41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment -41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) -41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) -41: -41: [----------] 5 tests from OptionsAssignerDoubleTest -41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue -41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat -41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) -41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue -41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) -41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) -41: -41: [----------] 9 tests from OptionsAssignerStringTest -41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue -41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray -41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue -41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue -41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) -41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector -41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) -41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) -41: -41: [----------] 6 tests from OptionsAssignerEnumTest -41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue -41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues -41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange -41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) -41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector -41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) -41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) -41: -41: [----------] 8 tests from RepeatingOptionSectionTest -41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance -41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption -41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance -41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue -41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances -41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault -41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault -41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) -41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections -41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) -41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) -41: -41: [----------] 1 test from TimeUnitManagerTest -41: [ RUN ] TimeUnitManagerTest.BasicOperations -41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) -41: [----------] 1 test from TimeUnitManagerTest (0 ms total) -41: -41: [----------] 4 tests from TimeUnitBehaviorTest -41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue -41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues -41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources -41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) -41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks -41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) -41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) -41: -41: [----------] 2 tests from TreeValueSupportAssignTest -41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree -41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) -41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays -41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) -41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) -41: -41: [----------] 1 test from TreeValueSupportAssignErrorTest -41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue -41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) -41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) -41: -41: [----------] 5 tests from TreeValueSupportCheckTest -41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty -41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree -41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 -41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 -41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) -41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue -41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) -41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) -41: -41: [----------] 6 tests from TreeValueSupportAdjustTest -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues -41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues -41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues -41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) -41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues -41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) -41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) -41: -41: [----------] 7 tests from TreeValueSupportTest -41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption -41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption -41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsInt64Option -41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsStringOption -41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsFloatOption -41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption -41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) -41: [ RUN ] TreeValueSupportTest.SupportsEnumOption -41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) -41: [----------] 7 tests from TreeValueSupportTest (0 ms total) -41: -41: [----------] Global test environment tear-down -41: [==========] 112 tests from 18 test suites ran. (4 ms total) -41: [ PASSED ] 112 tests. -41/92 Test #41: OptionsUnitTests .......................... Passed 0.02 sec -test 42 - Start 42: PbcutilUnitTest - -42: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" -42: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pbcutil/tests -42: Test timeout computed to be: 30 -42: [==========] Running 37 tests from 5 test suites. -42: [----------] Global test environment set-up. -42: [----------] 1 test from ShiftTest -42: [ RUN ] ShiftTest.CoordinateShiftWorks -42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) -42: [----------] 1 test from ShiftTest (0 ms total) -42: -42: [----------] 2 tests from MShift -42: [ RUN ] MShift.shiftsAndUnshifts -42: [ OK ] MShift.shiftsAndUnshifts (0 ms) -42: [ RUN ] MShift.shiftsAndUnshiftsSelf -42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) -42: [----------] 2 tests from MShift (0 ms total) -42: -42: [----------] 5 tests from PbcTest -42: [ RUN ] PbcTest.CalcShiftsWorks -42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) -42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox -42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox -42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox -42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) -42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf -42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) -42: [----------] 5 tests from PbcTest (0 ms total) -42: -42: [----------] 2 tests from PbcEnumsTest -42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect -42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) -42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect -42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) -42: [----------] 2 tests from PbcEnumsTest (0 ms total) -42: -42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) -42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 -42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) -42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (5 ms total) -42: -42: [----------] Global test environment tear-down -42: [==========] 37 tests from 5 test suites ran. (6 ms total) -42: [ PASSED ] 37 tests. -42/92 Test #42: PbcutilUnitTest ........................... Passed 0.02 sec -test 43 - Start 43: RandomUnitTests - -43: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" -43: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/random/tests -43: Test timeout computed to be: 30 -43: [==========] Running 44 tests from 10 test suites. -43: [----------] Global test environment set-up. -43: [----------] 4 tests from ExponentialDistributionTest -43: [ RUN ] ExponentialDistributionTest.Output -43: [ OK ] ExponentialDistributionTest.Output (0 ms) -43: [ RUN ] ExponentialDistributionTest.Logical -43: [ OK ] ExponentialDistributionTest.Logical (0 ms) -43: [ RUN ] ExponentialDistributionTest.Reset -43: [ OK ] ExponentialDistributionTest.Reset (0 ms) -43: [ RUN ] ExponentialDistributionTest.AltParam -43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) -43: -43: [----------] 4 tests from GammaDistributionTest -43: [ RUN ] GammaDistributionTest.Output -43: [ OK ] GammaDistributionTest.Output (0 ms) -43: [ RUN ] GammaDistributionTest.Logical -43: [ OK ] GammaDistributionTest.Logical (0 ms) -43: [ RUN ] GammaDistributionTest.Reset -43: [ OK ] GammaDistributionTest.Reset (0 ms) -43: [ RUN ] GammaDistributionTest.AltParam -43: [ OK ] GammaDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from GammaDistributionTest (0 ms total) -43: -43: [----------] 4 tests from NormalDistributionTest -43: [ RUN ] NormalDistributionTest.Output -43: [ OK ] NormalDistributionTest.Output (0 ms) -43: [ RUN ] NormalDistributionTest.Logical -43: [ OK ] NormalDistributionTest.Logical (0 ms) -43: [ RUN ] NormalDistributionTest.Reset -43: [ OK ] NormalDistributionTest.Reset (0 ms) -43: [ RUN ] NormalDistributionTest.AltParam -43: [ OK ] NormalDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from NormalDistributionTest (0 ms total) -43: -43: [----------] 1 test from SeedTest -43: [ RUN ] SeedTest.makeRandomSeed -43: [ OK ] SeedTest.makeRandomSeed (0 ms) -43: [----------] 1 test from SeedTest (0 ms total) -43: -43: [----------] 6 tests from TabulatedNormalDistributionTest -43: [ RUN ] TabulatedNormalDistributionTest.Output14 -43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Output16 -43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 -43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Logical -43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.Reset -43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) -43: [ RUN ] TabulatedNormalDistributionTest.AltParam -43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) -43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) -43: -43: [----------] 1 test from TabulatedNormalDistributionTableTest -43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties -43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) -43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) -43: -43: [----------] 6 tests from ThreeFry2x64Test -43: [ RUN ] ThreeFry2x64Test.Logical -43: [ OK ] ThreeFry2x64Test.Logical (0 ms) -43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence -43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) -43: [ RUN ] ThreeFry2x64Test.Reseed -43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) -43: [ RUN ] ThreeFry2x64Test.Discard -43: [ OK ] ThreeFry2x64Test.Discard (0 ms) -43: [ RUN ] ThreeFry2x64Test.InvalidCounter -43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) -43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter -43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) -43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) -43: -43: [----------] 4 tests from UniformIntDistributionTest -43: [ RUN ] UniformIntDistributionTest.Output -43: [ OK ] UniformIntDistributionTest.Output (0 ms) -43: [ RUN ] UniformIntDistributionTest.Logical -43: [ OK ] UniformIntDistributionTest.Logical (0 ms) -43: [ RUN ] UniformIntDistributionTest.Reset -43: [ OK ] UniformIntDistributionTest.Reset (0 ms) -43: [ RUN ] UniformIntDistributionTest.AltParam -43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) -43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) -43: -43: [----------] 5 tests from UniformRealDistributionTest -43: [ RUN ] UniformRealDistributionTest.GenerateCanonical -43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) -43: [ RUN ] UniformRealDistributionTest.Output -43: [ OK ] UniformRealDistributionTest.Output (0 ms) -43: [ RUN ] UniformRealDistributionTest.Logical -43: [ OK ] UniformRealDistributionTest.Logical (0 ms) -43: [ RUN ] UniformRealDistributionTest.Reset -43: [ OK ] UniformRealDistributionTest.Reset (0 ms) -43: [ RUN ] UniformRealDistributionTest.AltParam -43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) -43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) -43: -43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) -43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 -43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) -43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) -43: -43: [----------] Global test environment tear-down -43: [==========] 44 tests from 10 test suites ran. (2 ms total) -43: [ PASSED ] 44 tests. -43/92 Test #43: RandomUnitTests ........................... Passed 0.01 sec -test 44 - Start 44: RestraintTests - -44: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/RestraintTests.xml" -44: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/restraint/tests -44: Test timeout computed to be: 30 -44: [==========] Running 1 test from 1 test suite. -44: [----------] Global test environment set-up. -44: [----------] 1 test from RestraintManager -44: [ RUN ] RestraintManager.restraintList -44: [ OK ] RestraintManager.restraintList (0 ms) -44: [----------] 1 test from RestraintManager (0 ms total) -44: -44: [----------] Global test environment tear-down -44: [==========] 1 test from 1 test suite ran. (0 ms total) -44: [ PASSED ] 1 test. -44/92 Test #44: RestraintTests ............................ Passed 0.01 sec -test 45 - Start 45: TableUnitTests - -45: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TableUnitTests.xml" -45: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tables/tests -45: Test timeout computed to be: 30 -45: [==========] Running 20 tests from 2 test suites. -45: [----------] Global test environment set-up. -45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable -45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput -45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) -45: [ RUN ] SplineTableTest/0.Sinc -45: [ OK ] SplineTableTest/0.Sinc (0 ms) -45: [ RUN ] SplineTableTest/0.LJ12 -45: [ OK ] SplineTableTest/0.LJ12 (8 ms) -45: [ RUN ] SplineTableTest/0.PmeCorrection -45: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) -45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput -45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) -45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr -45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) -45: [ RUN ] SplineTableTest/0.TwoFunctions -45: [ OK ] SplineTableTest/0.TwoFunctions (13 ms) -45: [ RUN ] SplineTableTest/0.ThreeFunctions -45: [ OK ] SplineTableTest/0.ThreeFunctions (14 ms) -45: [ RUN ] SplineTableTest/0.Simd -45: [ OK ] SplineTableTest/0.Simd (2 ms) -45: [ RUN ] SplineTableTest/0.SimdTwoFunctions -45: [ OK ] SplineTableTest/0.SimdTwoFunctions (13 ms) -45: [----------] 10 tests from SplineTableTest/0 (55 ms total) -45: -45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable -45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput -45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) -45: [ RUN ] SplineTableTest/1.Sinc -45: [ OK ] SplineTableTest/1.Sinc (0 ms) -45: [ RUN ] SplineTableTest/1.LJ12 -45: [ OK ] SplineTableTest/1.LJ12 (18 ms) -45: [ RUN ] SplineTableTest/1.PmeCorrection -45: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) -45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput -45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) -45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr -45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) -45: [ RUN ] SplineTableTest/1.TwoFunctions -45: [ OK ] SplineTableTest/1.TwoFunctions (35 ms) -45: [ RUN ] SplineTableTest/1.ThreeFunctions -45: [ OK ] SplineTableTest/1.ThreeFunctions (38 ms) -45: [ RUN ] SplineTableTest/1.Simd -45: [ OK ] SplineTableTest/1.Simd (7 ms) -45: [ RUN ] SplineTableTest/1.SimdTwoFunctions -45: [ OK ] SplineTableTest/1.SimdTwoFunctions (30 ms) -45: [----------] 10 tests from SplineTableTest/1 (133 ms total) -45: -45: [----------] Global test environment tear-down -45: [==========] 20 tests from 2 test suites ran. (189 ms total) -45: [ PASSED ] 20 tests. -45/92 Test #45: TableUnitTests ............................ Passed 0.24 sec -test 46 - Start 46: TaskAssignmentUnitTests - -46: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" -46: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment/tests -46: Test timeout computed to be: 30 -46: [==========] Running 3 tests from 2 test suites. -46: [----------] Global test environment set-up. -46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest -46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork -46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) -46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid -46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) -46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) -46: -46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest -46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow -46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) -46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) -46: -46: [----------] Global test environment tear-down -46: [==========] 3 tests from 2 test suites ran. (0 ms total) -46: [ PASSED ] 3 tests. -46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.01 sec -test 47 - Start 47: GmxTimingTests - -47: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" -47: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/timing/tests -47: Test timeout computed to be: 30 -47: [==========] Running 6 tests from 1 test suite. -47: [----------] Global test environment set-up. -47: [----------] 6 tests from TimingTest -47: [ RUN ] TimingTest.ElementCountingWorks -47: [ OK ] TimingTest.ElementCountingWorks (0 ms) -47: [ RUN ] TimingTest.ElementNoCountingWorks -47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) -47: [ RUN ] TimingTest.SubElementCountingWorks -47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) -47: [ RUN ] TimingTest.SubElementNoCountingWorks -47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) -47: [ RUN ] TimingTest.RunWallCycle -47: [ OK ] TimingTest.RunWallCycle (1 ms) -47: [ RUN ] TimingTest.RunWallCycleSub -47: [ OK ] TimingTest.RunWallCycleSub (0 ms) -47: [----------] 6 tests from TimingTest (1 ms total) -47: -47: [----------] Global test environment tear-down -47: [==========] 6 tests from 1 test suite ran. (1 ms total) -47: [ PASSED ] 6 tests. -47/92 Test #47: GmxTimingTests ............................ Passed 0.01 sec -test 48 - Start 48: TopologyTest - -48: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TopologyTest.xml" -48: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/topology/tests -48: Test timeout computed to be: 30 -48: [==========] Running 153 tests from 10 test suites. -48: [----------] Global test environment set-up. -48: [----------] 3 tests from PdbAtomEntryTest -48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry -48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) -48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac -48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) -48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry -48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) -48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) -48: -48: [----------] 3 tests from ExclusionBlockTest -48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks -48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) -48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka -48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) -48: [ RUN ] ExclusionBlockTest.MergeExclusions -48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) -48: [----------] 3 tests from ExclusionBlockTest (0 ms total) -48: -48: [----------] 6 tests from InteractionListTest -48: [ RUN ] InteractionListTest.EmptyWorks -48: [ OK ] InteractionListTest.EmptyWorks (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionArray -48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms -48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) -48: [ RUN ] InteractionListTest.CanAddInteractionPointer -48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) -48: [ RUN ] InteractionListTest.CanAddListToOtherList -48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) -48: [ RUN ] InteractionListTest.ClearingWorks -48: [ OK ] InteractionListTest.ClearingWorks (0 ms) -48: [----------] 6 tests from InteractionListTest (0 ms total) -48: -48: [----------] 3 tests from IndexTest -48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) -48: [ RUN ] IndexTest.WriteIndexWorks -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.WriteIndexWorks (28 ms) -48: [ RUN ] IndexTest.WriteAndReadIndexWorks -48: -48: WARNING: Masses and atomic (Van der Waals) radii will be guessed -48: based on residue and atom names, since they could not be -48: definitively assigned from the information in your input -48: files. These guessed numbers might deviate from the mass -48: and radius of the atom type. Please check the output -48: files if necessary. Note, that this functionality may -48: be removed in a future GROMACS version. Please, consider -48: using another file format for your input. -48: -48: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) -48: [----------] 3 tests from IndexTest (32 ms total) -48: -48: [----------] 4 tests from MtopTest -48: [ RUN ] MtopTest.RangeBasedLoop -48: [ OK ] MtopTest.RangeBasedLoop (0 ms) -48: [ RUN ] MtopTest.Operators -48: [ OK ] MtopTest.Operators (0 ms) -48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms -48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) -48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly -48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) -48: [----------] 4 tests from MtopTest (0 ms total) -48: -48: [----------] 2 tests from IListRangeTest -48: [ RUN ] IListRangeTest.RangeBasedLoopWorks -48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) -48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction -48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) -48: [----------] 2 tests from IListRangeTest (0 ms total) -48: -48: [----------] 13 tests from StringTableTest -48: [ RUN ] StringTableTest.AddSingleEntry -48: [ OK ] StringTableTest.AddSingleEntry (0 ms) -48: [ RUN ] StringTableTest.CanAccessWithAt -48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) -48: [ RUN ] StringTableTest.CanAccessWithBracket -48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) -48: [ RUN ] StringTableTest.ThrowsOutOfRange -48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) -48: [ RUN ] StringTableTest.StringCompareIsCorrect -48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) -48: [ RUN ] StringTableTest.AddTwoDistinctEntries -48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) -48: [ RUN ] StringTableTest.TryToAddDuplicates -48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) -48: [ RUN ] StringTableTest.AddLargeNumberOfEntries -48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) -48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable -48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) -48: [ RUN ] StringTableTest.CanWriteToBuffer -48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) -48: [ RUN ] StringTableTest.Roundtrip -48: [ OK ] StringTableTest.Roundtrip (0 ms) -48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices -48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) -48: [ RUN ] StringTableTest.CanCopyToLegacyTable -48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) -48: [----------] 13 tests from StringTableTest (2 ms total) -48: -48: [----------] 6 tests from LegacySymtabTest -48: [ RUN ] LegacySymtabTest.EmptyOnOpen -48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) -48: [ RUN ] LegacySymtabTest.AddSingleEntry -48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) -48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries -48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) -48: [ RUN ] LegacySymtabTest.TryToAddDuplicates -48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) -48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries -48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) -48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable -48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) -48: [----------] 6 tests from LegacySymtabTest (0 ms total) -48: -48: [----------] 5 tests from TopSortTest -48: [ RUN ] TopSortTest.WorksOnEmptyIdef -48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) -48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction -48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) -48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) -48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) -48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions -48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) -48: [----------] 5 tests from TopSortTest (0 ms total) -48: -48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) -48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 -48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) -48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (8 ms total) -48: -48: [----------] Global test environment tear-down -48: [==========] 153 tests from 10 test suites ran. (43 ms total) -48: [ PASSED ] 153 tests. -48: -48: YOU HAVE 1 DISABLED TEST -48: -48/92 Test #48: TopologyTest .............................. Passed 0.06 sec -test 49 - Start 49: PullTest - -49: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/PullTest.xml" -49: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling/tests -49: Test timeout computed to be: 30 -49: [==========] Running 10 tests from 1 test suite. -49: [----------] Global test environment set-up. -49: [----------] 10 tests from PullTest -49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox -49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox -49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox -49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox -49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) -49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox -49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) -49: [ RUN ] PullTest.TransformationCoordSimple -49: [ OK ] PullTest.TransformationCoordSimple (0 ms) -49: [ RUN ] PullTest.TransformationCoordAdvanced -49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) -49: [ RUN ] PullTest.TransformationCoordTime -49: [ OK ] PullTest.TransformationCoordTime (0 ms) -49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed -49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) -49: [ RUN ] PullTest.TransformationCoordDummyExpression -49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) -49: [----------] 10 tests from PullTest (0 ms total) -49: -49: [----------] Global test environment tear-down -49: [==========] 10 tests from 1 test suite ran. (0 ms total) -49: [ PASSED ] 10 tests. -49/92 Test #49: PullTest .................................. Passed 0.01 sec -test 50 - Start 50: SimdUnitTests - -50: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" -50: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/simd/tests -50: Test timeout computed to be: 30 -50: [==========] Running 247 tests from 19 test suites. -50: [----------] Global test environment set-up. -50: [----------] 6 tests from SimdBootstrapTest -50: [ RUN ] SimdBootstrapTest.loadStore -50: [ OK ] SimdBootstrapTest.loadStore (0 ms) -50: [ RUN ] SimdBootstrapTest.loadU -50: [ OK ] SimdBootstrapTest.loadU (0 ms) -50: [ RUN ] SimdBootstrapTest.storeU -50: [ OK ] SimdBootstrapTest.storeU (0 ms) -50: [ RUN ] SimdBootstrapTest.loadStoreI -50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) -50: [ RUN ] SimdBootstrapTest.loadUI -50: [ OK ] SimdBootstrapTest.loadUI (0 ms) -50: [ RUN ] SimdBootstrapTest.storeUI -50: [ OK ] SimdBootstrapTest.storeUI (0 ms) -50: [----------] 6 tests from SimdBootstrapTest (0 ms total) -50: -50: [----------] 41 tests from SimdScalarTest -50: [ RUN ] SimdScalarTest.load -50: [ OK ] SimdScalarTest.load (0 ms) -50: [ RUN ] SimdScalarTest.loadU -50: [ OK ] SimdScalarTest.loadU (0 ms) -50: [ RUN ] SimdScalarTest.store -50: [ OK ] SimdScalarTest.store (0 ms) -50: [ RUN ] SimdScalarTest.storeU -50: [ OK ] SimdScalarTest.storeU (0 ms) -50: [ RUN ] SimdScalarTest.setZero -50: [ OK ] SimdScalarTest.setZero (0 ms) -50: [ RUN ] SimdScalarTest.andNot -50: [ OK ] SimdScalarTest.andNot (0 ms) -50: [ RUN ] SimdScalarTest.fma -50: [ OK ] SimdScalarTest.fma (0 ms) -50: [ RUN ] SimdScalarTest.fms -50: [ OK ] SimdScalarTest.fms (0 ms) -50: [ RUN ] SimdScalarTest.fnma -50: [ OK ] SimdScalarTest.fnma (0 ms) -50: [ RUN ] SimdScalarTest.fnms -50: [ OK ] SimdScalarTest.fnms (0 ms) -50: [ RUN ] SimdScalarTest.maskAdd -50: [ OK ] SimdScalarTest.maskAdd (0 ms) -50: [ RUN ] SimdScalarTest.maskzMul -50: [ OK ] SimdScalarTest.maskzMul (0 ms) -50: [ RUN ] SimdScalarTest.maskzFma -50: [ OK ] SimdScalarTest.maskzFma (0 ms) -50: [ RUN ] SimdScalarTest.abs -50: [ OK ] SimdScalarTest.abs (0 ms) -50: [ RUN ] SimdScalarTest.max -50: [ OK ] SimdScalarTest.max (0 ms) -50: [ RUN ] SimdScalarTest.min -50: [ OK ] SimdScalarTest.min (0 ms) -50: [ RUN ] SimdScalarTest.round -50: [ OK ] SimdScalarTest.round (0 ms) -50: [ RUN ] SimdScalarTest.trunc -50: [ OK ] SimdScalarTest.trunc (0 ms) -50: [ RUN ] SimdScalarTest.reduce -50: [ OK ] SimdScalarTest.reduce (0 ms) -50: [ RUN ] SimdScalarTest.testBits -50: [ OK ] SimdScalarTest.testBits (0 ms) -50: [ RUN ] SimdScalarTest.anyTrue -50: [ OK ] SimdScalarTest.anyTrue (0 ms) -50: [ RUN ] SimdScalarTest.selectByMask -50: [ OK ] SimdScalarTest.selectByMask (0 ms) -50: [ RUN ] SimdScalarTest.selectByNotMask -50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) -50: [ RUN ] SimdScalarTest.blend -50: [ OK ] SimdScalarTest.blend (0 ms) -50: [ RUN ] SimdScalarTest.cvtR2I -50: [ OK ] SimdScalarTest.cvtR2I (0 ms) -50: [ RUN ] SimdScalarTest.cvttR2I -50: [ OK ] SimdScalarTest.cvttR2I (0 ms) -50: [ RUN ] SimdScalarTest.cvtI2R -50: [ OK ] SimdScalarTest.cvtI2R (0 ms) -50: [ RUN ] SimdScalarTest.cvtF2D -50: [ OK ] SimdScalarTest.cvtF2D (0 ms) -50: [ RUN ] SimdScalarTest.cvtD2D -50: [ OK ] SimdScalarTest.cvtD2D (0 ms) -50: [ RUN ] SimdScalarTest.loadI -50: [ OK ] SimdScalarTest.loadI (0 ms) -50: [ RUN ] SimdScalarTest.loadUI -50: [ OK ] SimdScalarTest.loadUI (0 ms) -50: [ RUN ] SimdScalarTest.storeI -50: [ OK ] SimdScalarTest.storeI (0 ms) -50: [ RUN ] SimdScalarTest.storeUI -50: [ OK ] SimdScalarTest.storeUI (0 ms) -50: [ RUN ] SimdScalarTest.andNotI -50: [ OK ] SimdScalarTest.andNotI (0 ms) -50: [ RUN ] SimdScalarTest.testBitsI -50: [ OK ] SimdScalarTest.testBitsI (0 ms) -50: [ RUN ] SimdScalarTest.selectByMaskI -50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) -50: [ RUN ] SimdScalarTest.selectByNotMaskI -50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) -50: [ RUN ] SimdScalarTest.blendI -50: [ OK ] SimdScalarTest.blendI (0 ms) -50: [ RUN ] SimdScalarTest.cvtB2IB -50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) -50: [ RUN ] SimdScalarTest.cvtIB2B -50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) -50: [ RUN ] SimdScalarTest.expandScalarsToTriplets -50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) -50: [----------] 41 tests from SimdScalarTest (0 ms total) -50: -50: [----------] 8 tests from SimdScalarUtilTest -50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU -50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU -50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) -50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU -50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose -50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) -50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum -50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) -50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) -50: -50: [----------] 37 tests from SimdScalarMathTest -50: [ RUN ] SimdScalarMathTest.copysign -50: [ OK ] SimdScalarMathTest.copysign (0 ms) -50: [ RUN ] SimdScalarMathTest.invsqrtPair -50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) -50: [ RUN ] SimdScalarMathTest.inv -50: [ OK ] SimdScalarMathTest.inv (0 ms) -50: [ RUN ] SimdScalarMathTest.maskzInvsqrt -50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) -50: [ RUN ] SimdScalarMathTest.log -50: [ OK ] SimdScalarMathTest.log (0 ms) -50: [ RUN ] SimdScalarMathTest.exp2 -50: [ OK ] SimdScalarMathTest.exp2 (0 ms) -50: [ RUN ] SimdScalarMathTest.exp -50: [ OK ] SimdScalarMathTest.exp (0 ms) -50: [ RUN ] SimdScalarMathTest.erf -50: [ OK ] SimdScalarMathTest.erf (0 ms) -50: [ RUN ] SimdScalarMathTest.erfc -50: [ OK ] SimdScalarMathTest.erfc (0 ms) -50: [ RUN ] SimdScalarMathTest.sincos -50: [ OK ] SimdScalarMathTest.sincos (0 ms) -50: [ RUN ] SimdScalarMathTest.sin -50: [ OK ] SimdScalarMathTest.sin (0 ms) -50: [ RUN ] SimdScalarMathTest.cos -50: [ OK ] SimdScalarMathTest.cos (0 ms) -50: [ RUN ] SimdScalarMathTest.tan -50: [ OK ] SimdScalarMathTest.tan (0 ms) -50: [ RUN ] SimdScalarMathTest.asin -50: [ OK ] SimdScalarMathTest.asin (0 ms) -50: [ RUN ] SimdScalarMathTest.acos -50: [ OK ] SimdScalarMathTest.acos (0 ms) -50: [ RUN ] SimdScalarMathTest.atan -50: [ OK ] SimdScalarMathTest.atan (0 ms) -50: [ RUN ] SimdScalarMathTest.atan2 -50: [ OK ] SimdScalarMathTest.atan2 (0 ms) -50: [ RUN ] SimdScalarMathTest.pmeForceCorrection -50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) -50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection -50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) -50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy -50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.invSingleAccuracy -50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy -50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.logSingleAccuracy -50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy -50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.expSingleAccuracy -50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy -50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy -50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy -50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy -50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy -50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy -50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy -50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy -50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy -50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy -50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy -50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy -50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -50: [----------] 37 tests from SimdScalarMathTest (0 ms total) -50: -50: [----------] 1 test from SimdTest -50: [ RUN ] SimdTest.GmxAligned -50: [ OK ] SimdTest.GmxAligned (0 ms) -50: [----------] 1 test from SimdTest (0 ms total) -50: -50: [----------] 42 tests from SimdFloatingpointTest -50: [ RUN ] SimdFloatingpointTest.setZero -50: [ OK ] SimdFloatingpointTest.setZero (0 ms) -50: [ RUN ] SimdFloatingpointTest.set -50: [ OK ] SimdFloatingpointTest.set (0 ms) -50: [ RUN ] SimdFloatingpointTest.add -50: [ OK ] SimdFloatingpointTest.add (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskAdd -50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) -50: [ RUN ] SimdFloatingpointTest.sub -50: [ OK ] SimdFloatingpointTest.sub (0 ms) -50: [ RUN ] SimdFloatingpointTest.mul -50: [ OK ] SimdFloatingpointTest.mul (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzMul -50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) -50: [ RUN ] SimdFloatingpointTest.fma -50: [ OK ] SimdFloatingpointTest.fma (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzFma -50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) -50: [ RUN ] SimdFloatingpointTest.fms -50: [ OK ] SimdFloatingpointTest.fms (0 ms) -50: [ RUN ] SimdFloatingpointTest.fnma -50: [ OK ] SimdFloatingpointTest.fnma (0 ms) -50: [ RUN ] SimdFloatingpointTest.fnms -50: [ OK ] SimdFloatingpointTest.fnms (0 ms) -50: [ RUN ] SimdFloatingpointTest.abs -50: [ OK ] SimdFloatingpointTest.abs (0 ms) -50: [ RUN ] SimdFloatingpointTest.neg -50: [ OK ] SimdFloatingpointTest.neg (0 ms) -50: [ RUN ] SimdFloatingpointTest.and -50: [ OK ] SimdFloatingpointTest.and (0 ms) -50: [ RUN ] SimdFloatingpointTest.or -50: [ OK ] SimdFloatingpointTest.or (0 ms) -50: [ RUN ] SimdFloatingpointTest.xor -50: [ OK ] SimdFloatingpointTest.xor (0 ms) -50: [ RUN ] SimdFloatingpointTest.andNot -50: [ OK ] SimdFloatingpointTest.andNot (0 ms) -50: [ RUN ] SimdFloatingpointTest.max -50: [ OK ] SimdFloatingpointTest.max (0 ms) -50: [ RUN ] SimdFloatingpointTest.min -50: [ OK ] SimdFloatingpointTest.min (0 ms) -50: [ RUN ] SimdFloatingpointTest.round -50: [ OK ] SimdFloatingpointTest.round (0 ms) -50: [ RUN ] SimdFloatingpointTest.roundMode -50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) -50: [ RUN ] SimdFloatingpointTest.trunc -50: [ OK ] SimdFloatingpointTest.trunc (0 ms) -50: [ RUN ] SimdFloatingpointTest.frexp -50: [ OK ] SimdFloatingpointTest.frexp (0 ms) -50: [ RUN ] SimdFloatingpointTest.ldexp -50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) -50: [ RUN ] SimdFloatingpointTest.rsqrt -50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzRsqrt -50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) -50: [ RUN ] SimdFloatingpointTest.rcp -50: [ OK ] SimdFloatingpointTest.rcp (0 ms) -50: [ RUN ] SimdFloatingpointTest.maskzRcp -50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask -50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) -50: [ RUN ] SimdFloatingpointTest.selectByNotMask -50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpNe -50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpLe -50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) -50: [ RUN ] SimdFloatingpointTest.cmpLt -50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) -50: [ RUN ] SimdFloatingpointTest.testBits -50: [ OK ] SimdFloatingpointTest.testBits (0 ms) -50: [ RUN ] SimdFloatingpointTest.andB -50: [ OK ] SimdFloatingpointTest.andB (0 ms) -50: [ RUN ] SimdFloatingpointTest.orB -50: [ OK ] SimdFloatingpointTest.orB (0 ms) -50: [ RUN ] SimdFloatingpointTest.anyTrueB -50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) -50: [ RUN ] SimdFloatingpointTest.blend -50: [ OK ] SimdFloatingpointTest.blend (0 ms) -50: [ RUN ] SimdFloatingpointTest.reduce -50: [ OK ] SimdFloatingpointTest.reduce (0 ms) -50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double -50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) -50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float -50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) -50: [----------] 42 tests from SimdFloatingpointTest (0 ms total) -50: -50: [----------] 13 tests from SimdFloatingpointUtilTest -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping -50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets -50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 -50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) -50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum -50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) -50: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) -50: -50: [----------] 23 tests from SimdIntegerTest -50: [ RUN ] SimdIntegerTest.setZero -50: [ OK ] SimdIntegerTest.setZero (0 ms) -50: [ RUN ] SimdIntegerTest.set -50: [ OK ] SimdIntegerTest.set (0 ms) -50: [ RUN ] SimdIntegerTest.add -50: [ OK ] SimdIntegerTest.add (0 ms) -50: [ RUN ] SimdIntegerTest.sub -50: [ OK ] SimdIntegerTest.sub (0 ms) -50: [ RUN ] SimdIntegerTest.mul -50: [ OK ] SimdIntegerTest.mul (0 ms) -50: [ RUN ] SimdIntegerTest.and -50: [ OK ] SimdIntegerTest.and (0 ms) -50: [ RUN ] SimdIntegerTest.andNot -50: [ OK ] SimdIntegerTest.andNot (0 ms) -50: [ RUN ] SimdIntegerTest.or -50: [ OK ] SimdIntegerTest.or (0 ms) -50: [ RUN ] SimdIntegerTest.xor -50: [ OK ] SimdIntegerTest.xor (0 ms) -50: [ RUN ] SimdIntegerTest.extract -50: [ OK ] SimdIntegerTest.extract (0 ms) -50: [ RUN ] SimdIntegerTest.cvtR2I -50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) -50: [ RUN ] SimdIntegerTest.cvttR2I -50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) -50: [ RUN ] SimdIntegerTest.cvtI2R -50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) -50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask -50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) -50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask -50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) -50: [ RUN ] SimdIntegerTest.cmpLt -50: [ OK ] SimdIntegerTest.cmpLt (0 ms) -50: [ RUN ] SimdIntegerTest.testBits -50: [ OK ] SimdIntegerTest.testBits (0 ms) -50: [ RUN ] SimdIntegerTest.andB -50: [ OK ] SimdIntegerTest.andB (0 ms) -50: [ RUN ] SimdIntegerTest.orB -50: [ OK ] SimdIntegerTest.orB (0 ms) -50: [ RUN ] SimdIntegerTest.anyTrue -50: [ OK ] SimdIntegerTest.anyTrue (0 ms) -50: [ RUN ] SimdIntegerTest.blend -50: [ OK ] SimdIntegerTest.blend (0 ms) -50: [ RUN ] SimdIntegerTest.cvtB2IB -50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) -50: [ RUN ] SimdIntegerTest.cvtIB2B -50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) -50: [----------] 23 tests from SimdIntegerTest (0 ms total) -50: -50: [----------] 56 tests from SimdMathTest -50: [ RUN ] SimdMathTest.generateTestPointsDouble -50: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) -50: [ RUN ] SimdMathTest.copysign -50: [ OK ] SimdMathTest.copysign (0 ms) -50: [ RUN ] SimdMathTest.invsqrt -50: [ OK ] SimdMathTest.invsqrt (0 ms) -50: [ RUN ] SimdMathTest.maskzInvsqrt -50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) -50: [ RUN ] SimdMathTest.invsqrtPair -50: [ OK ] SimdMathTest.invsqrtPair (0 ms) -50: [ RUN ] SimdMathTest.sqrt -50: [ OK ] SimdMathTest.sqrt (1 ms) -50: [ RUN ] SimdMathTest.sqrtUnsafe -50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) -50: [ RUN ] SimdMathTest.inv -50: [ OK ] SimdMathTest.inv (1 ms) -50: [ RUN ] SimdMathTest.maskzInv -50: [ OK ] SimdMathTest.maskzInv (0 ms) -50: [ RUN ] SimdMathTest.cbrt -50: [ OK ] SimdMathTest.cbrt (0 ms) -50: [ RUN ] SimdMathTest.invcbrt -50: [ OK ] SimdMathTest.invcbrt (1 ms) -50: [ RUN ] SimdMathTest.log2 -50: [ OK ] SimdMathTest.log2 (0 ms) -50: [ RUN ] SimdMathTest.log -50: [ OK ] SimdMathTest.log (0 ms) -50: [ RUN ] SimdMathTest.exp2 -50: [ OK ] SimdMathTest.exp2 (1 ms) -50: [ RUN ] SimdMathTest.exp2Unsafe -50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) -50: [ RUN ] SimdMathTest.exp -50: [ OK ] SimdMathTest.exp (1 ms) -50: [ RUN ] SimdMathTest.expUnsafe -50: [ OK ] SimdMathTest.expUnsafe (0 ms) -50: [ RUN ] SimdMathTest.pow -50: [ OK ] SimdMathTest.pow (0 ms) -50: [ RUN ] SimdMathTest.powUnsafe -50: [ OK ] SimdMathTest.powUnsafe (0 ms) -50: [ RUN ] SimdMathTest.erf -50: [ OK ] SimdMathTest.erf (0 ms) -50: [ RUN ] SimdMathTest.erfc -50: [ OK ] SimdMathTest.erfc (0 ms) -50: [ RUN ] SimdMathTest.sin -50: [ OK ] SimdMathTest.sin (0 ms) -50: [ RUN ] SimdMathTest.cos -50: [ OK ] SimdMathTest.cos (0 ms) -50: [ RUN ] SimdMathTest.tan -50: [ OK ] SimdMathTest.tan (1 ms) -50: [ RUN ] SimdMathTest.asin -50: [ OK ] SimdMathTest.asin (0 ms) -50: [ RUN ] SimdMathTest.acos -50: [ OK ] SimdMathTest.acos (0 ms) -50: [ RUN ] SimdMathTest.atan -50: [ OK ] SimdMathTest.atan (0 ms) -50: [ RUN ] SimdMathTest.atan2 -50: [ OK ] SimdMathTest.atan2 (0 ms) -50: [ RUN ] SimdMathTest.pmeForceCorrection -50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) -50: [ RUN ] SimdMathTest.pmePotentialCorrection -50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) -50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy -50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy -50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sqrtSingleAccuracy -50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.invSingleAccuracy -50: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) -50: [ RUN ] SimdMathTest.cbrtSingleAccuracy -50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy -50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) -50: [ RUN ] SimdMathTest.log2SingleAccuracy -50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.logSingleAccuracy -50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.exp2SingleAccuracy -50: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) -50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe -50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.expSingleAccuracy -50: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) -50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.powSingleAccuracy -50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe -50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) -50: [ RUN ] SimdMathTest.erfSingleAccuracy -50: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.erfcSingleAccuracy -50: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.sinSingleAccuracy -50: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.cosSingleAccuracy -50: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.tanSingleAccuracy -50: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.asinSingleAccuracy -50: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.acosSingleAccuracy -50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.atanSingleAccuracy -50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.atan2SingleAccuracy -50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy -50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy -50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -50: [----------] 56 tests from SimdMathTest (34 ms total) -50: -50: [----------] 1 test from EmptyArrayRefTest -50: [ RUN ] EmptyArrayRefTest.IsEmpty -50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -50: [----------] 1 test from EmptyArrayRefTest (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) -50: -50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks -50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) -50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks -50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) -50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) -50: -50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefReadWriteTest/0.Assignment -50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) -50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) -50: -50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefReadWriteTest/1.Assignment -50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) -50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) -50: -50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefArithmeticTest/0.Basic -50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) -50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) -50: -50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef -50: [ RUN ] ArrayRefArithmeticTest/1.Basic -50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) -50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) -50: -50: [----------] 3 tests from SimdVectorOperationsTest -50: [ RUN ] SimdVectorOperationsTest.iprod -50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) -50: [ RUN ] SimdVectorOperationsTest.norm2 -50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) -50: [ RUN ] SimdVectorOperationsTest.cprod -50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) -50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) -50: -50: [----------] Global test environment tear-down -50: [==========] 247 tests from 19 test suites ran. (35 ms total) -50: [ PASSED ] 247 tests. -50/92 Test #50: SimdUnitTests ............................. Passed 0.16 sec -test 51 - Start 51: CompatibilityHelpersTests - -51: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" -51: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/compat/tests -51: Test timeout computed to be: 30 -51: [==========] Running 9 tests from 6 test suites. -51: [----------] Global test environment set-up. -51: [----------] 4 tests from TemplateMPTest -51: [ RUN ] TemplateMPTest.MpWithIndexInt -51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexIntBad -51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexBool -51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) -51: [ RUN ] TemplateMPTest.MpWithIndexEnum -51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) -51: [----------] 4 tests from TemplateMPTest (0 ms total) -51: -51: [----------] 1 test from NotNullConstruction -51: [ RUN ] NotNullConstruction.Works -51: [ OK ] NotNullConstruction.Works (0 ms) -51: [----------] 1 test from NotNullConstruction (0 ms total) -51: -51: [----------] 1 test from NotNullCasting -51: [ RUN ] NotNullCasting.Works -51: [ OK ] NotNullCasting.Works (0 ms) -51: [----------] 1 test from NotNullCasting (0 ms total) -51: -51: [----------] 1 test from NotNullAssignment -51: [ RUN ] NotNullAssignment.Works -51: [ OK ] NotNullAssignment.Works (0 ms) -51: [----------] 1 test from NotNullAssignment (0 ms total) -51: -51: [----------] 1 test from MakeNotNull -51: [ RUN ] MakeNotNull.Works -51: [ OK ] MakeNotNull.Works (0 ms) -51: [----------] 1 test from MakeNotNull (0 ms total) -51: -51: [----------] 1 test from NotNull -51: [ RUN ] NotNull.WorksInContainers -51: [ OK ] NotNull.WorksInContainers (0 ms) -51: [----------] 1 test from NotNull (0 ms total) -51: -51: [----------] Global test environment tear-down -51: [==========] 9 tests from 6 test suites ran. (0 ms total) -51: [ PASSED ] 9 tests. -51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.01 sec -test 52 - Start 52: GmxAnaTest - -52: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" -52: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxana/tests -52: Test timeout computed to be: 600 -52: [==========] Running 31 tests from 4 test suites. -52: [----------] Global test environment set-up. -52: [----------] 7 tests from Entropy -52: [ RUN ] Entropy.Schlitter_300_NoLinear -52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) -52: [ RUN ] Entropy.Schlitter_300_Linear -52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear -52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear -52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) -52: [ RUN ] Entropy.QuasiHarmonic_200_Linear -52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) -52: [ RUN ] Entropy.EntropyCompare_200_Linear -52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) -52: [ RUN ] Entropy.EntropyCompare_300_Linear -52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) -52: [----------] 7 tests from Entropy (0 ms total) -52: -52: [----------] 2 tests from GmxChiTest -52: [ RUN ] GmxChiTest.gmxchiWorksWithAll -52: Analyzing from residue 1 to residue 11 -52: 10 residues with dihedrals found -52: 46 dihedrals found -52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -52: j after resetting (nr. active dihedrals) = 46 -52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg -52: Now calculating transitions... -52: Total number of transitions: 0 -52: Now printing out transitions and OPs... -52: Now printing out rotamer occupancies... -52: Now calculating Chi product trajectories... -52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg -52: [ OK ] GmxChiTest.gmxchiWorksWithAll (2105 ms) -52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN -52: Analyzing from residue 2 to residue 6 -52: 5 residues with dihedrals found -52: 23 dihedrals found -52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -52: j after resetting (nr. active dihedrals) = 23 -52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg -52: Now calculating transitions... -52: Total number of transitions: 0 -52: Now printing out transitions and OPs... -52: Now printing out rotamer occupancies... -52: Now calculating Chi product trajectories... -52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg -52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (863 ms) -52: [----------] 2 tests from GmxChiTest (3040 ms total) -52: -52: [----------] 10 tests from MindistTest -52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (3 ms) -52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 2: 'atom3' -52: Selected 3: 'atoms12' -52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) -52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) -52: [ RUN ] MindistTest.mindistPicksUpContacts -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.mindistPicksUpContacts (53 ms) -52: [ RUN ] MindistTest.ngWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.ngWorks (0 ms) -52: [ RUN ] MindistTest.groupWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 3: 'atoms12' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.groupWorks (112 ms) -52: [ RUN ] MindistTest.maxDistWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 2: 'atom3' -52: Selected 3: 'atoms12' -52: [ OK ] MindistTest.maxDistWorks (101 ms) -52: [ RUN ] MindistTest.noPbcWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 0: 'atom1' -52: Selected 1: 'atom2' -52: [ OK ] MindistTest.noPbcWorks (0 ms) -52: [ RUN ] MindistTest.resPerTimeWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 3: 'atoms12' -52: Selected 2: 'atom3' -52: [ OK ] MindistTest.resPerTimeWorks (27 ms) -52: [ RUN ] MindistTest.matrixWorks -52: Group 0 ( atom1) has 1 elements -52: Group 1 ( atom2) has 1 elements -52: Group 2 ( atom3) has 1 elements -52: Group 3 ( atoms12) has 2 elements -52: Group 4 ( atoms23) has 2 elements -52: Group 5 ( atoms123) has 3 elements -52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -52: Reading frame 0 time 0.000 Last frame 0 time 0.000 -52: Selected 5: 'atoms123' -52: Special case: making distance matrix between all atoms in group atoms123 -52: [ OK ] MindistTest.matrixWorks (0 ms) -52: [----------] 10 tests from MindistTest (302 ms total) -52: -52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: trr version: GMX_trn_file (single precision) -52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (122 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -52: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) -52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 -52: Group 0 ( System) has 6 elements -52: Group 1 ( Water) has 6 elements -52: Group 2 ( SOL) has 6 elements -52: Select a group: Reading frame 0 time 0.000 -52: WARNING: If there are molecules in the input trajectory file -52: that are broken across periodic boundaries, they -52: cannot be made whole (or treated as whole) without -52: you providing a run input file. -52: -52: Reading frame 1 time 1.000 Last frame 1 time 1.000 -52: -52: WARNING: Masses and atomic (Van der Waals) radii will be guessed -52: based on residue and atom names, since they could not be -52: definitively assigned from the information in your input -52: files. These guessed numbers might deviate from the mass -52: and radius of the atom type. Please check the output -52: files if necessary. Note, that this functionality may -52: be removed in a future GROMACS version. Please, consider -52: using another file format for your input. -52: -52: Selected 0: 'System' -52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) -52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (138 ms total) -52: -52: [----------] Global test environment tear-down -52: [==========] 31 tests from 4 test suites ran. (3481 ms total) -52: [ PASSED ] 31 tests. -52/92 Test #52: GmxAnaTest ................................ Passed 3.50 sec -test 53 - Start 53: GmxPreprocessTests - -53: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" -53: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests -53: Test timeout computed to be: 1920 -53: [==========] Running 215 tests from 15 test suites. -53: [----------] Global test environment set-up. -53: [----------] 1 test from ConvertInteractionsTest -53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks -53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) -53: [----------] 1 test from ConvertInteractionsTest (0 ms total) -53: -53: [----------] 4 tests from GenconfTest -53: [ RUN ] GenconfTest.nbox_Works -53: [ OK ] GenconfTest.nbox_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_norenumber_Works -53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_dist_Works -53: [ OK ] GenconfTest.nbox_dist_Works (0 ms) -53: [ RUN ] GenconfTest.nbox_rot_Works -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: center of geometry: 1.733667, 1.477000, 0.905167 -53: [ OK ] GenconfTest.nbox_rot_Works (0 ms) -53: [----------] 4 tests from GenconfTest (2 ms total) -53: -53: [----------] 2 tests from GenionTest -53: [ RUN ] GenionTest.HighConcentrationIonPlacement -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -53: buffer. The cluster pair list does have a buffering effect, but choosing -53: a larger rlist might be necessary for good energy conservation. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -53: < 0 -53: -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: Generating 1-4 interactions: fudge = 0.5 -53: Number of degrees of freedom in T-Coupling group rest is 1308.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -53: You are using a plain Coulomb cut-off, which might produce artifacts. -53: You might want to consider using PME electrostatics. -53: -53: -53: -53: There were 4 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -53: Group 0 ( System) has 653 elements -53: Group 1 ( Water) has 648 elements -53: Group 2 ( SOL) has 648 elements -53: Group 3 ( non-Water) has 5 elements -53: Group 4 ( Other) has 5 elements -53: Group 5 ( METH) has 5 elements -53: Select a group: Number of (3-atomic) solvent molecules: 216 -53: Using random seed 1997. -53: Replacing solvent molecule 56 (atom 168) with NA -53: Replacing solvent molecule 120 (atom 360) with NA -53: Replacing solvent molecule 182 (atom 546) with NA -53: Replacing solvent molecule 71 (atom 213) with NA -53: Replacing solvent molecule 189 (atom 567) with CL -53: Replacing solvent molecule 54 (atom 162) with CL -53: Replacing solvent molecule 155 (atom 465) with CL -53: Replacing solvent molecule 99 (atom 297) with CL -53: -53: Setting the LD random seed to -1124352135 -53: -53: Generated 331705 of the 331705 non-bonded parameter combinations -53: -53: Generated 331705 of the 331705 1-4 parameter combinations -53: -53: Excluding 2 bonded neighbours molecule type 'SOL' -53: -53: Excluding 3 bonded neighbours molecule type 'methane' -53: -53: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -53: Analysing residue names: -53: There are: 216 Water residues -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: This run will generate roughly 0 Mb of data -53: Will try to add 4 NA ions and 4 CL ions. -53: Select a continuous group of solvent molecules -53: Selected 1: 'Water' -53: [ OK ] GenionTest.HighConcentrationIonPlacement (439 ms) -53: [ RUN ] GenionTest.NoIonPlacement -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -53: buffer. The cluster pair list does have a buffering effect, but choosing -53: a larger rlist might be necessary for good energy conservation. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -53: < 0 -53: -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: Generating 1-4 interactions: fudge = 0.5 -53: Number of degrees of freedom in T-Coupling group rest is 1308.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -53: You are using a plain Coulomb cut-off, which might produce artifacts. -53: You might want to consider using PME electrostatics. -53: -53: -53: -53: There were 4 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -53: No ions to add, will just copy input configuration. -53: Setting the LD random seed to -336265426 -53: -53: Generated 331705 of the 331705 non-bonded parameter combinations -53: -53: Generated 331705 of the 331705 1-4 parameter combinations -53: -53: Excluding 2 bonded neighbours molecule type 'SOL' -53: -53: Excluding 3 bonded neighbours molecule type 'methane' -53: -53: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -53: Analysing residue names: -53: There are: 216 Water residues -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GenionTest.NoIonPlacement (419 ms) -53: [----------] 2 tests from GenionTest (858 ms total) -53: -53: [----------] 1 test from GenRestrTest -53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated -53: -53: Reading structure file -53: Group 0 ( System) has 156 elements -53: Group 1 ( Protein) has 156 elements -53: Group 2 ( Protein-H) has 75 elements -53: Group 3 ( C-alpha) has 10 elements -53: Group 4 ( Backbone) has 30 elements -53: Group 5 ( MainChain) has 40 elements -53: Group 6 ( MainChain+Cb) has 49 elements -53: Group 7 ( MainChain+H) has 52 elements -53: Group 8 ( SideChain) has 104 elements -53: Group 9 ( SideChain-H) has 35 elements -53: Select a group: Select group to position restrain -53: Selected 3: 'C-alpha' -53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) -53: [----------] 1 test from GenRestrTest (1 ms total) -53: -53: [----------] 9 tests from PreprocessingAtomTypesTest -53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate -53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid -53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks -53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks -53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry -53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound -53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound -53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber -53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) -53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber -53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) -53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) -53: -53: [----------] 10 tests from PreprocessingBondAtomTypeTest -53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate -53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid -53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks -53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks -53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry -53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType -53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound -53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound -53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber -53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) -53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber -53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) -53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) -53: -53: [----------] 3 tests from GromppDirectiveTest -53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives.top, line 59]: -53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 9.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -53: Setting the LD random seed to -537036834 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -141329473 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (120 ms) -53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives.top, line 59]: -53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have -53: coefficients that do not sum to zero. This does not affect the simulation -53: and can be ignored, unless you are comparing potential energy values with -53: other force field ports and/or MD software. -53: First such dihedral in molecule A, involving atoms 0 2 1 3 -53: -53: -53: NOTE 2 [file directives.top, line 59]: -53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 9.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 3 NOTEs -53: Setting the LD random seed to -18978 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 1859903312 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (107 ms) -53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy -53: Setting the LD random seed to 2079714175 -53: -53: Generated 10 of the 10 non-bonded parameter combinations -53: -53: Generated 10 of the 10 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -404049926 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (236 ms) -53: [----------] 3 tests from GromppDirectiveTest (463 ms total) -53: -53: [----------] 6 tests from InsertMoleculesTest -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 8 atoms)! -53: -53: Added 1 molecules (out of 1 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro -53: -53: Output configuration contains 8 atoms in 4 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 success (now 6 atoms)! -53: Try 4 success (now 8 atoms)! -53: Try 5 success (now 10 atoms)! -53: -53: Added 5 molecules (out of 5 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro -53: -53: Output configuration contains 10 atoms in 10 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 success (now 6 atoms)! -53: Try 4 success (now 8 atoms)! -53: Try 5 success (now 10 atoms)! -53: -53: Added 5 molecules (out of 5 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro -53: -53: Output configuration contains 10 atoms in 10 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (130 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 8 atoms)! -53: Try 2 success (now 10 atoms)! -53: -53: Added 2 molecules (out of 2 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro -53: -53: Output configuration contains 10 atoms in 4 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement -53: Reading solute configuration -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Try 1 success (now 650 atoms)! -53: Try 2 success (now 652 atoms)! -53: Try 3 success (now 654 atoms)! -53: Try 4 success (now 656 atoms)! -53: -53: Added 4 molecules (out of 4 requested) -53: Replaced 8 residues (24 atoms) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro -53: -53: Output configuration contains 632 atoms in 212 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (3 ms) -53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Using random seed 1997 -53: Read 4 positions from file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat -53: -53: Try 1 success (now 2 atoms)! -53: Try 2 success (now 4 atoms)! -53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) -53: Try 13 success (now 6 atoms)! -53: -53: Added 3 molecules (out of 4 requested) -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro -53: -53: Output configuration contains 6 atoms in 3 residues -53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) -53: [----------] 6 tests from InsertMoleculesTest (138 ms total) -53: -53: [----------] 3 tests from MassRepartitioning -53: [ RUN ] MassRepartitioning.ValidCaseWorks -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) -53: [ RUN ] MassRepartitioning.UnboundGivesWarning -53: -53: WARNING 1 [file unknown]: -53: The are 1 atoms that have a mass below the mass repartitioning limit but -53: are not bound. These masses cannot be repartitioned. -53: -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) -53: [ RUN ] MassRepartitioning.LightPartnerGivesError -53: -53: ERROR 1 [file unknown]: -53: Light atoms are bound to at least one atom that has a too low mass for -53: repartitioning -53: -53: The smallest mass in the system is 2, setting the minimum mass to 6 -53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) -53: [----------] 3 tests from MassRepartitioning (0 ms total) -53: -53: [----------] 35 tests from GetIrTest -53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines -53: Ignoring obsolete mdp entry 'title' -53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) -53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals -53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (76 ms) -53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) -53: [ RUN ] GetIrTest.RejectsValueWithoutKey -53: [ OK ] GetIrTest.RejectsValueWithoutKey (4 ms) -53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue -53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (4 ms) -53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) -53: [ RUN ] GetIrTest.AcceptsEmptyLines -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstenergy -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: Setting nstcalcenergy (100) equal to nstenergy (5) -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstpcouple -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -53: Pressure coupling incorrect number of values (I need exactly 1) -53: -53: -53: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -53: Pressure coupling incorrect number of values (I need exactly 1) -53: -53: -53: ERROR 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: With multiple time stepping, nstpcouple should be a multiple of -53: mts-factor -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: -53: ERROR 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: The Berendsen barostat does not generate any strictly correct ensemble, -53: and should not be used for new production simulations (in our opinion). -53: We recommend using the C-rescale barostat instead. -53: -53: -53: ERROR 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -53: compressibility must be > 0 when using pressure coupling Berendsen -53: -53: -53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) -53: [ RUN ] GetIrTest.MtsCheckNstdhdl -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: Setting nstcalcenergy (100) equal to nstdhdl (5) -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: -53: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -53: Lambda state must be set, either with init-lambda-state or with -53: init-lambda -53: -53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) -53: [ RUN ] GetIrTest.MtsCheckSDNotSupported -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -53: Multiple time stepping is only supported with integrator md -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricField -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricField (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) -53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) -53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys -53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) -53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) -53: [ RUN ] GetIrTest.RejectsImplicitSolventYes -53: [ OK ] GetIrTest.RejectsImplicitSolventYes (3 ms) -53: [ RUN ] GetIrTest.AcceptsMimic -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsMimic (2 ms) -53: [ RUN ] GetIrTest.AcceptsTransformationCoord -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: -53: pull-coord2 has a non-zero force constant and is also referenced in -53: pull-coord1-expression. Make sure that this is intended. In most use -53: cases, the pull coordinates referenced by a transformation coordinate -53: should have their force constant set to zero. -53: -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) -53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: -53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) -53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: -53: pull-coord2 can not use pull-coord1 in the transformation since this is a -53: constraint -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) -53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: -53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry -53: 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) -53: [ RUN ] GetIrTest.MissingTransformationCoordExpression -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: -53: pull-coord1-expression not set for pull coordinate of geometry -53: 'transformation' -53: -53: -53: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: -53: For a correct single-point energy evaluation with nsteps = 0, use -53: continuation = yes to avoid constraining the input coordinates. -53: -53: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: -53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, -53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of -53: in total 100001 steps. This is not compatible with using soft-core -53: potentials. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -53: won't change anymore after step 100000 until the end of the simulation -53: after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -53: won't change anymore after step 100000 until the end of the simulation -53: after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: -53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda -53: components won't change anymore after step 100000 until the end of the -53: simulation after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta -53: -53: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: -53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda -53: components won't change anymore after step 100000 until the end of the -53: simulation after 100001 steps. -53: -53: -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) -53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta -53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) -53: [----------] 35 tests from GetIrTest (136 ms total) -53: -53: [----------] 6 tests from SolvateTest -53: [ RUN ] SolvateTest.cs_box_Works -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 1x1x1 boxes -53: Solvent box contains 270 atoms in 90 residues -53: Removed 129 solvent atoms due to solvent-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 47 residues -53: Generated solvent containing 141 atoms in 47 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro -53: -53: Output configuration contains 141 atoms in 47 residues -53: Volume : 1.331 (nm^3) -53: Density : 1056.36 (g/l) -53: Number of solvent molecules: 47 -53: -53: [ OK ] SolvateTest.cs_box_Works (3 ms) -53: [ RUN ] SolvateTest.cs_cp_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 886 residues -53: Generated solvent containing 2658 atoms in 886 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro -53: -53: Output configuration contains 2664 atoms in 888 residues -53: Volume : 27.2709 (nm^3) -53: Density : 974.777 (g/l) -53: Number of solvent molecules: 886 -53: -53: [ OK ] SolvateTest.cs_cp_Works (13 ms) -53: [ RUN ] SolvateTest.cs_cp_p_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 886 residues -53: Generated solvent containing 2658 atoms in 886 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro -53: -53: Output configuration contains 2664 atoms in 888 residues -53: Volume : 27.2709 (nm^3) -53: Density : 974.777 (g/l) -53: Number of solvent molecules: 886 -53: -53: Processing topology -53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) -53: [ OK ] SolvateTest.cs_cp_p_Works (136 ms) -53: [ RUN ] SolvateTest.shell_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 3660 atoms in 1220 residues -53: Removed 987 solvent atoms due to solvent-solvent overlap -53: Removed 1902 solvent atoms more than 1.000000 nm from solute. -53: Removed 15 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 252 residues -53: Generated solvent containing 756 atoms in 252 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro -53: -53: Output configuration contains 762 atoms in 254 residues -53: Volume : 27.2709 (nm^3) -53: Density : 279.3 (g/l) -53: Number of solvent molecules: 252 -53: -53: [ OK ] SolvateTest.shell_Works (86 ms) -53: [ RUN ] SolvateTest.update_Topology_Works -53: Reading solute configuration -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 3x3x3 boxes -53: Solvent box contains 14952 atoms in 4984 residues -53: Removed 2787 solvent atoms due to solvent-solvent overlap -53: Removed 30 solvent atoms due to solute-solvent overlap -53: Sorting configuration -53: Found 2 different molecule types: -53: HOH ( 3 atoms): 1876 residues -53: SOL ( 3 atoms): 2169 residues -53: Generated solvent containing 0 atoms in 0 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro -53: -53: Output configuration contains 12141 atoms in 4047 residues -53: Volume : 125 (nm^3) -53: Density : 968.963 (g/l) -53: Number of solvent molecules: 4045 -53: -53: Processing topology -53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -53: [ OK ] SolvateTest.update_Topology_Works (383 ms) -53: [ RUN ] SolvateTest.cs_pdb_big_box_Works -53: Reading solvent configuration -53: -53: Initialising inter-atomic distances... -53: -53: WARNING: Masses and atomic (Van der Waals) radii will be guessed -53: based on residue and atom names, since they could not be -53: definitively assigned from the information in your input -53: files. These guessed numbers might deviate from the mass -53: and radius of the atom type. Please check the output -53: files if necessary. Note, that this functionality may -53: be removed in a future GROMACS version. Please, consider -53: using another file format for your input. -53: -53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -53: from the source below. This means the results may be different -53: compared to previous GROMACS versions. -53: -53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -53: A. Bondi -53: van der Waals Volumes and Radii -53: J. Phys. Chem. (1964) -53: DOI: 10.1021/j100785a001 -53: -------- -------- --- Thank You --- -------- -------- -53: -53: Generating solvent configuration -53: Will generate new solvent configuration of 2x2x2 boxes -53: Solvent box contains 1218 atoms in 406 residues -53: Removed 555 solvent atoms due to solvent-solvent overlap -53: Sorting configuration -53: Found 1 molecule type: -53: SOL ( 3 atoms): 221 residues -53: Generated solvent containing 663 atoms in 221 residues -53: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro -53: -53: Output configuration contains 663 atoms in 221 residues -53: Volume : 8 (nm^3) -53: Density : 826.409 (g/l) -53: Number of solvent molecules: 221 -53: -53: [ OK ] SolvateTest.cs_pdb_big_box_Works (39 ms) -53: [----------] 6 tests from SolvateTest (663 ms total) -53: -53: [----------] 1 test from TopDirTests -53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize -53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) -53: [----------] 1 test from TopDirTests (0 ms total) -53: -53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N -53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) -53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -53: Skipping interaction type that does not represent a interaction with parameters converted in grompp -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) -53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (2 ms total) -53: -53: [----------] 16 tests from CorrectVelocity/MaxwellTest -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (1 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) -53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 -53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) -53: [----------] 16 tests from CorrectVelocity/MaxwellTest (10 ms total) -53: -53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 -53: Setting the LD random seed to -203436546 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (151 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 -53: Setting the LD random seed to 402223550 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (230 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -134226825 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -8650753 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (339 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -638583941 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -138983241 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (404 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -11666209 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -17957121 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (161 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -673339161 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -639795491 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (281 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 -53: Setting the LD random seed to 2013134782 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (416 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 -53: Setting the LD random seed to -1077029393 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -14705251 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (127 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 -53: Setting the LD random seed to -1647325188 -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (276 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 -53: Setting the LD random seed to -2687794 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 2008471515 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (388 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 -53: Setting the LD random seed to -135792641 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -268437637 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (295 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 -53: Setting the LD random seed to -942671883 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to 1862270655 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (317 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 -53: Setting the LD random seed to 1914699519 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1318196833 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (269 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 -53: Setting the LD random seed to -1023606827 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -4460653 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (72 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 -53: Setting the LD random seed to 2130179817 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1075847929 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (327 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 -53: Setting the LD random seed to -809648265 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -604669066 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (477 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -1078219387 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1116161 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (57 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -5312865 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -170296905 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (432 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 -53: Setting the LD random seed to -33886278 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (156 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 -53: Setting the LD random seed to 1576451642 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1362216195 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (310 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 -53: Setting the LD random seed to -604074119 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (328 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 -53: Ignoring obsolete mdp entry 'title' -53: Generating 1-4 interactions: fudge = 0.5 -53: -53: NOTE 1 [file directives-cmap.top, line 114]: -53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -53: any other atom in the same moleculetype. Although technically this might -53: not cause issues in a simulation, this often means that the user forgot -53: to add a bond/potential/constraint or put multiple molecules in the same -53: moleculetype definition by mistake. Run with -v to get information for -53: each atom. -53: -53: Number of degrees of freedom in T-Coupling group rest is 12.00 -53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -53: -53: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: -53: NVE simulation: will use the initial temperature of 300.000 K for -53: determining the Verlet buffer size -53: -53: -53: There were 2 NOTEs -53: Setting the LD random seed to -1132851 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: -53: Excluding 0 bonded neighbours molecule type 'A' -53: -53: Setting gen_seed to -1612840970 -53: -53: Velocities were taken from a Maxwell distribution at 300 K -53: Analysing residue names: -53: There are: 1 Other residues -53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -53: -53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -53: -53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -53: -53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -53: -53: Note that mdrun will redetermine rlist based on the actual pair-list setup -53: -53: This run will generate roughly 0 Mb of data -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (107 ms) -53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 -53: Setting the LD random seed to -1082786818 -53: -53: Generated 3 of the 3 non-bonded parameter combinations -53: -53: Generated 3 of the 3 1-4 parameter combinations -53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (309 ms) -53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (6238 ms total) -53: -53: [----------] Global test environment tear-down -53: [==========] 215 tests from 15 test suites ran. (8516 ms total) -53: [ PASSED ] 175 tests. -53: [ SKIPPED ] 40 tests, listed below: -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -53/92 Test #53: GmxPreprocessTests ........................ Passed 8.53 sec -test 54 - Start 54: Pdb2gmx1Test - -54: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" -54: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests -54: Test timeout computed to be: 1920 -54: [==========] Running 30 tests from 1 test suite. -54: [----------] Global test environment set-up. -54: [----------] 30 tests from Oplsaa/Pdb2gmxTest -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (401 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (203 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (441 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (381 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (799 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (415 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (176 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip3p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (299 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (161 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (238 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (177 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (150 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (519 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (187 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (362 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (77 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (340 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip4p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (486 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 0 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (78 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 0 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (82 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 0 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (270 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 0 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (274 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 0 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (140 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 25 donors and 23 acceptors were found. -54: There are 41 hydrogen bonds -54: Will use HISE for residue 8 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS3 HIS8 -54: SG9 NE251 -54: HIS8 NE251 1.055 -54: MET12 SD83 0.763 0.990 -54: Marked 124 virtual sites -54: Added 16 dummy masses -54: Added 26 new constraints -54: Before cleaning: 653 pairs -54: Before cleaning: 663 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 128 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (128 atoms, 16 residues) -54: -54: Identified residue ALA2 as a starting terminus. -54: -54: Identified residue SER17 as a ending terminus. -54: Start terminus ALA-2: NH3+ -54: End terminus SER-17: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 252 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 254, now 254 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 663 dihedrals, 51 impropers, 457 angles -54: 650 pairs, 254 bonds and 130 virtual sites -54: -54: Total mass 1846.112 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (90 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 30 donors and 22 acceptors were found. -54: There are 36 hydrogen bonds -54: Will use HISE for residue 29 -54: Will use HISE for residue 32 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS27 HIS29 -54: SG90 NE2111 -54: HIS29 NE2111 0.987 -54: HIS32 NE2135 1.590 1.155 -54: Marked 132 virtual sites -54: Added 10 dummy masses -54: Added 19 new constraints -54: Before cleaning: 748 pairs -54: Before cleaning: 778 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 149 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (149 atoms, 16 residues) -54: -54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue THR18 as a starting terminus. -54: -54: Identified residue PHE33 as a ending terminus. -54: Start terminus THR-18: NH3+ -54: End terminus PHE-33: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 281 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 290, now 290 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 778 dihedrals, 72 impropers, 516 angles -54: 736 pairs, 290 bonds and 133 virtual sites -54: -54: Total mass 2088.357 a.m.u. -54: -54: Total charge 1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (248 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 22 acceptors were found. -54: There are 26 hydrogen bonds -54: Will use HISE for residue 45 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS45 -54: NE295 -54: MET46 SD102 1.078 -54: Marked 123 virtual sites -54: Added 22 dummy masses -54: Added 35 new constraints -54: Before cleaning: 676 pairs -54: Before cleaning: 696 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 132 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (132 atoms, 16 residues) -54: -54: Identified residue ALA34 as a starting terminus. -54: -54: Identified residue ALA49 as a ending terminus. -54: Start terminus ALA-34: NH3+ -54: End terminus ALA-49: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 255 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 261, now 261 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 696 dihedrals, 56 impropers, 472 angles -54: 667 pairs, 261 bonds and 132 virtual sites -54: -54: Total mass 1861.128 a.m.u. -54: -54: Total charge -1.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (54 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 22 donors and 21 acceptors were found. -54: There are 30 hydrogen bonds -54: Will use HISE for residue 60 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: HIS60 -54: NE285 -54: CYS62 SG98 0.803 -54: Marked 111 virtual sites -54: Added 18 dummy masses -54: Added 31 new constraints -54: Before cleaning: 603 pairs -54: Before cleaning: 618 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -54: -54: chain #res #atoms -54: -54: 1 ' ' 16 117 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 (117 atoms, 16 residues) -54: -54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -54: -54: Identified residue LYS50 as a starting terminus. -54: -54: Identified residue PRO65 as a ending terminus. -54: Start terminus LYS-50: NH3+ -54: End terminus PRO-65: PRO-COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 16 residues with 228 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 232, now 232 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 618 dihedrals, 48 impropers, 419 angles -54: 597 pairs, 232 bonds and 116 virtual sites -54: -54: Total mass 1662.883 a.m.u. -54: -54: Total charge 0.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (116 ms) -54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -54: All occupancies are one -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -54: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -54: Analysing hydrogen-bonding network for automated assignment of histidine -54: protonation. 89 donors and 98 acceptors were found. -54: There are 129 hydrogen bonds -54: Will use HISE for residue 31 -54: Will use HISE for residue 51 -54: 9 out of 9 lines of specbond.dat converted successfully -54: Special Atom Distance matrix: -54: CYS25 HIS31 HIS51 -54: SG14 NE264 NE2226 -54: HIS31 NE264 1.921 -54: HIS51 NE2226 1.498 2.650 -54: CYS80 SG477 0.207 1.984 1.570 -54: Linking CYS-25 SG-14 and CYS-80 SG-477... -54: Marked 447 virtual sites -54: Added 58 dummy masses -54: Added 101 new constraints -54: Before cleaning: 2499 pairs -54: Before cleaning: 2524 dihedrals -54: Using the Oplsaa force field in directory oplsaa.ff -54: -54: going to rename oplsaa.ff/aminoacids.r2b -54: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -54: -54: Analyzing pdb file -54: Splitting chemical chains based on TER records or chain id changing. -54: -54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -54: -54: chain #res #atoms -54: -54: 1 'A' 58 488 -54: -54: All occupancies are one -54: -54: Reading residue database... (Oplsaa) -54: -54: Processing chain 1 'A' (488 atoms, 58 residues) -54: -54: Identified residue ASN24 as a starting terminus. -54: -54: Identified residue ARG81 as a ending terminus. -54: Start terminus ASN-24: NH3+ -54: End terminus ARG-81: COO- -54: -54: Checking for duplicate atoms.... -54: -54: Generating any missing hydrogen atoms and/or adding termini. -54: -54: Now there are 58 residues with 936 atoms -54: -54: Making bonds... -54: -54: Number of bonds was 951, now 951 -54: -54: Generating angles, dihedrals and pairs... -54: -54: Making cmap torsions... -54: -54: There are 2524 dihedrals, 208 impropers, 1704 angles -54: 2469 pairs, 951 bonds and 462 virtual sites -54: -54: Total mass 6908.578 a.m.u. -54: -54: Total charge -6.000 e -54: -54: Writing topology -54: -54: Writing coordinate file... -54: -54: --------- PLEASE NOTE ------------ -54: -54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -54: -54: The Oplsaa force field and the tip5p water model are used. -54: -54: --------- ETON ESAELP ------------ -54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (162 ms) -54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (7437 ms total) -54: -54: [----------] Global test environment tear-down -54: [==========] 30 tests from 1 test suite ran. (7437 ms total) -54: [ PASSED ] 30 tests. -54/92 Test #54: Pdb2gmx1Test .............................. Passed 7.45 sec -test 55 - Start 55: Pdb2gmx2Test - -55: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" -55: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests -55: Test timeout computed to be: 1920 -55: [==========] Running 40 tests from 2 test suites. -55: [----------] Global test environment set-up. -55: [----------] 20 tests from G43a1/Pdb2gmxTest -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (101 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (249 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (201 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (64 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (145 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 37 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 37 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (339 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 53 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 51 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (97 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 36 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 36 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (159 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 33 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 31 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (149 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 146 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 137 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (131 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (124 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (114 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (84 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (233 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (137 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 37 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 305 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 165 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 172, now 167 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 77 impropers, 241 angles -55: 267 pairs, 167 bonds and 37 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (132 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 53 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 429 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 202 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 216, now 211 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 134 impropers, 316 angles -55: 273 pairs, 211 bonds and 51 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (215 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 36 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 349 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 168 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 179, now 174 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 102 impropers, 260 angles -55: 242 pairs, 174 bonds and 36 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (147 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 33 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 299 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 150 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 159, now 154 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 80 impropers, 227 angles -55: 232 pairs, 154 bonds and 31 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (155 ms) -55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 146 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1256 dihedrals -55: Using the Gromos43a1 force field in directory gromos43a1.ff -55: -55: going to rename gromos43a1.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos43a1) -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 635 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 655, now 650 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 350 impropers, 955 angles -55: 972 pairs, 650 bonds and 137 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos43a1 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (104 ms) -55: [----------] 20 tests from G43a1/Pdb2gmxTest (3093 ms total) -55: -55: [----------] 20 tests from G53a6/Pdb2gmxTest -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (147 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (152 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (176 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (170 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (234 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 39 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 39 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (247 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 57 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 55 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (223 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 38 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 38 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (150 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 35 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 33 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (180 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 150 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 141 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spc water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (239 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 0 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (180 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 0 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (170 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 0 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (104 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 0 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (365 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 0 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (183 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 25 donors and 23 acceptors were found. -55: There are 41 hydrogen bonds -55: Will use HISE for residue 8 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS3 HIS8 -55: SG9 NE251 -55: HIS8 NE251 1.055 -55: MET12 SD83 0.763 0.990 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 39 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 267 pairs -55: Before cleaning: 312 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 128 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (128 atoms, 16 residues) -55: -55: Identified residue ALA2 as a starting terminus. -55: -55: Identified residue SER17 as a ending terminus. -55: Start terminus ALA-2: NH3+ -55: End terminus SER-17: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 167 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 174, now 169 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 90 dihedrals, 79 impropers, 245 angles -55: 267 pairs, 169 bonds and 39 virtual sites -55: -55: Total mass 1846.116 a.m.u. -55: -55: Total charge 0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (275 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 30 donors and 22 acceptors were found. -55: There are 36 hydrogen bonds -55: Will use HISE for residue 29 -55: Will use HISE for residue 32 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS27 HIS29 -55: SG90 NE2111 -55: HIS29 NE2111 0.987 -55: HIS32 NE2135 1.590 1.155 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 57 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 273 pairs -55: Before cleaning: 443 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 149 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (149 atoms, 16 residues) -55: -55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue THR18 as a starting terminus. -55: -55: Identified residue PHE33 as a ending terminus. -55: Start terminus THR-18: NH3+ -55: End terminus PHE-33: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 206 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 220, now 215 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 93 dihedrals, 138 impropers, 324 angles -55: 273 pairs, 215 bonds and 55 virtual sites -55: -55: Total mass 2088.361 a.m.u. -55: -55: Total charge 1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (126 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 22 acceptors were found. -55: There are 26 hydrogen bonds -55: Will use HISE for residue 45 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS45 -55: NE295 -55: MET46 SD102 1.078 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 38 virtual sites -55: Added 4 dummy masses -55: Added 8 new constraints -55: -55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 242 pairs -55: Before cleaning: 356 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 132 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (132 atoms, 16 residues) -55: -55: Identified residue ALA34 as a starting terminus. -55: -55: Identified residue ALA49 as a ending terminus. -55: Start terminus ALA-34: NH3+ -55: End terminus ALA-49: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 170 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 181, now 176 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 81 dihedrals, 104 impropers, 264 angles -55: 242 pairs, 176 bonds and 38 virtual sites -55: -55: Total mass 1861.132 a.m.u. -55: -55: Total charge -1.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (118 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 22 donors and 21 acceptors were found. -55: There are 30 hydrogen bonds -55: Will use HISE for residue 60 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: HIS60 -55: NE285 -55: CYS62 SG98 0.803 -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 35 virtual sites -55: Added 4 dummy masses -55: Added 10 new constraints -55: -55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 232 pairs -55: Before cleaning: 306 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -55: -55: chain #res #atoms -55: -55: 1 ' ' 16 117 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 (117 atoms, 16 residues) -55: -55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -55: -55: Identified residue LYS50 as a starting terminus. -55: -55: Identified residue PRO65 as a ending terminus. -55: Start terminus LYS-50: NH3+ -55: End terminus PRO-65: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 16 residues with 152 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 161, now 156 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 78 dihedrals, 82 impropers, 231 angles -55: 232 pairs, 156 bonds and 33 virtual sites -55: -55: Total mass 1662.887 a.m.u. -55: -55: Total charge -0.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (80 ms) -55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -55: All occupancies are one -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -55: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -55: Analysing hydrogen-bonding network for automated assignment of histidine -55: protonation. 89 donors and 98 acceptors were found. -55: There are 129 hydrogen bonds -55: Will use HISE for residue 31 -55: Will use HISE for residue 51 -55: 9 out of 9 lines of specbond.dat converted successfully -55: Special Atom Distance matrix: -55: CYS25 HIS31 HIS51 -55: SG14 NE264 NE2226 -55: HIS31 NE264 1.921 -55: HIS51 NE2226 1.498 2.650 -55: CYS80 SG477 0.207 1.984 1.570 -55: Linking CYS-25 SG-14 and CYS-80 SG-477... -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: -55: WARNING: Duplicate line found in or between hackblock and rtp entries -55: -55: Marked 150 virtual sites -55: Added 10 dummy masses -55: Added 29 new constraints -55: -55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom H used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: -55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -55: to an entry in the topology database, but the atom O used in -55: an interaction of type angle in that entry is not found in the -55: input file. Perhaps your atom and/or residue naming needs to be -55: fixed. -55: -55: -55: Before cleaning: 972 pairs -55: Before cleaning: 1270 dihedrals -55: Using the Gromos53a6 force field in directory gromos53a6.ff -55: -55: going to rename gromos53a6.ff/aminoacids.r2b -55: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -55: -55: Analyzing pdb file -55: Splitting chemical chains based on TER records or chain id changing. -55: -55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -55: -55: chain #res #atoms -55: -55: 1 'A' 58 488 -55: -55: All occupancies are one -55: -55: Reading residue database... (Gromos53a6) -55: -55: Using default: not generating all possible dihedrals -55: -55: Using default: excluding 3 bonded neighbors -55: -55: Using default: generating 1,4 H--H interactions -55: -55: Using default: removing proper dihedrals found on the same bond as a proper dihedral -55: -55: Processing chain 1 'A' (488 atoms, 58 residues) -55: -55: Identified residue ASN24 as a starting terminus. -55: -55: Identified residue ARG81 as a ending terminus. -55: Start terminus ASN-24: NH3+ -55: End terminus ARG-81: COO- -55: -55: Checking for duplicate atoms.... -55: -55: Generating any missing hydrogen atoms and/or adding termini. -55: -55: Now there are 58 residues with 639 atoms -55: -55: Making bonds... -55: -55: Number of bonds was 659, now 654 -55: -55: Generating angles, dihedrals and pairs... -55: -55: Making cmap torsions... -55: -55: There are 321 dihedrals, 354 impropers, 963 angles -55: 972 pairs, 654 bonds and 141 virtual sites -55: -55: Total mass 6908.582 a.m.u. -55: -55: Total charge -6.000 e -55: -55: Writing topology -55: -55: Writing coordinate file... -55: -55: --------- PLEASE NOTE ------------ -55: -55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -55: -55: The Gromos53a6 force field and the spce water model are used. -55: -55: --------- ETON ESAELP ------------ -55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (152 ms) -55: [----------] 20 tests from G53a6/Pdb2gmxTest (3683 ms total) -55: -55: [----------] Global test environment tear-down -55: [==========] 40 tests from 2 test suites ran. (6776 ms total) -55: [ PASSED ] 40 tests. -55/92 Test #55: Pdb2gmx2Test .............................. Passed 6.79 sec -test 56 - Start 56: Pdb2gmx3Test - -56: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" -56: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/gmxpreprocess/tests -56: Test timeout computed to be: 1920 -56: [==========] Running 39 tests from 6 test suites. -56: [----------] Global test environment set-up. -56: [----------] 10 tests from Amber/Pdb2gmxTest -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 653 pairs -56: Before cleaning: 691 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 255, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 691 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.132 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (146 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 748 pairs -56: Before cleaning: 788 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 291, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 788 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.366 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (195 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 676 pairs -56: Before cleaning: 727 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 262, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 727 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.124 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (135 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 603 pairs -56: Before cleaning: 634 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 233, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 634 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.888 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (378 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Before cleaning: 2499 pairs -56: Before cleaning: 2631 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 952, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2631 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.576 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (313 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 691 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 255, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 691 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.132 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (126 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 788 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 291, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 788 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.366 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (164 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 727 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 262, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 727 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.124 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (123 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 634 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 233, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 634 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.888 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (32 ms) -56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2631 dihedrals -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 952, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2631 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.576 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Amber99sb-ildn force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (200 ms) -56: [----------] 10 tests from Amber/Pdb2gmxTest (1818 ms total) -56: -56: [----------] 1 test from AmberTip4p/Pdb2gmxTest -56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -56: -56: going to rename amber99sb-ildn.ff/aminoacids.r2b -56: -56: going to rename amber99sb-ildn.ff/dna.r2b -56: -56: going to rename amber99sb-ildn.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... -56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 2 4 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Amber99sb-ildn) -56: -56: Processing chain 1 (4 atoms, 2 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 2 residues with 8 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 4, now 4 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 2 angles -56: 0 pairs, 4 bonds and 0 virtual sites -56: -56: Total mass 36.032 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. -56: -56: The Amber99sb-ildn force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (36 ms) -56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (36 ms total) -56: -56: [----------] 12 tests from Charmm/Pdb2gmxTest -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 663 dihedrals, 48 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.115 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 778 dihedrals, 49 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.361 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (94 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 696 dihedrals, 39 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.130 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (87 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 618 dihedrals, 38 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.885 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (270 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 56 cmap torsion pairs -56: -56: There are 2524 dihedrals, 149 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.566 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (344 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 39 pairs -56: Before cleaning: 39 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -56: Read 'GLU', 9 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -56: -56: chain #res #atoms -56: -56: 1 'X' 1 9 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'X' (9 atoms, 1 residues) -56: -56: Identified residue GLU1 as a starting terminus. -56: -56: Identified residue GLU1 as a ending terminus. -56: Start terminus GLU-1: NH3+ -56: End terminus GLU-1: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 1 residues with 18 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 17, now 17 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 39 dihedrals, 2 impropers, 30 angles -56: 39 pairs, 17 bonds and 0 virtual sites -56: -56: Total mass 146.123 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (75 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 663 dihedrals, 48 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.115 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (261 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 778 dihedrals, 49 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.361 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (158 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 696 dihedrals, 39 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.130 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (257 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 14 cmap torsion pairs -56: -56: There are 618 dihedrals, 38 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.885 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (176 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 56 cmap torsion pairs -56: -56: There are 2524 dihedrals, 149 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.566 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (693 ms) -56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Marked 8 virtual sites -56: Added 2 dummy masses -56: Added 3 new constraints -56: Before cleaning: 39 pairs -56: Before cleaning: 39 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -56: Read 'GLU', 9 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -56: -56: chain #res #atoms -56: -56: 1 'X' 1 9 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'X' (9 atoms, 1 residues) -56: -56: Identified residue GLU1 as a starting terminus. -56: -56: Identified residue GLU1 as a ending terminus. -56: Start terminus GLU-1: NH3+ -56: End terminus GLU-1: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 1 residues with 18 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 17, now 17 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 39 dihedrals, 2 impropers, 30 angles -56: 39 pairs, 17 bonds and 9 virtual sites -56: -56: Total mass 146.123 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (382 ms) -56: [----------] 12 tests from Charmm/Pdb2gmxTest (2881 ms total) -56: -56: [----------] 8 tests from ChainSep/Pdb2gmxTest -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 651 pairs -56: Before cleaning: 661 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: Start terminus PHE-6: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 258 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 258, now 258 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 10 cmap torsion pairs -56: -56: There are 661 dihedrals, 46 impropers, 463 angles -56: 648 pairs, 258 bonds and 0 virtual sites -56: -56: Total mass 1882.146 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (400 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 123 pairs -56: Before cleaning: 123 dihedrals -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 10 donors and 7 acceptors were found. -56: There are 7 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS8 -56: NE223 -56: MET12 SD55 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 317 pairs -56: Before cleaning: 322 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 4 28 -56: -56: 2 'B' 7 58 -56: -56: 3 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (28 atoms, 4 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 51 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 50, now 50 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 123 dihedrals, 9 impropers, 88 angles -56: 123 pairs, 50 bonds and 0 virtual sites -56: -56: Total mass 434.421 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (58 atoms, 7 residues) -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus PHE-6: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 7 residues with 124 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 125, now 125 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 5 cmap torsion pairs -56: -56: There are 322 dihedrals, 19 impropers, 227 angles -56: 314 pairs, 125 bonds and 0 virtual sites -56: -56: Total mass 846.083 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 51 atoms 4 residues -56: -56: Including chain 2 in system: 124 atoms 7 residues -56: -56: Including chain 3 in system: 83 atoms 5 residues -56: -56: Now there are 258 atoms and 16 residues -56: -56: Total mass in system 1882.146 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (21 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 651 pairs -56: Before cleaning: 661 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ILE-9: COO- -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 258 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 258, now 258 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 10 cmap torsion pairs -56: -56: There are 661 dihedrals, 46 impropers, 463 angles -56: 648 pairs, 258 bonds and 0 virtual sites -56: -56: Total mass 1882.146 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (295 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 10 donors and 12 acceptors were found. -56: There are 13 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 -56: SG9 -56: HIS8 NE251 1.055 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 288 pairs -56: Before cleaning: 293 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 152 pairs -56: Before cleaning: 152 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 8 61 -56: -56: 2 'B' 3 25 -56: -56: 3 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (61 atoms, 8 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ILE-9: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 8 residues with 114 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 115, now 115 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6 cmap torsion pairs -56: -56: There are 293 dihedrals, 23 impropers, 203 angles -56: 285 pairs, 115 bonds and 0 virtual sites -56: -56: Total mass 888.952 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (25 atoms, 3 residues) -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 61 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 60, now 60 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 152 dihedrals, 5 impropers, 112 angles -56: 152 pairs, 60 bonds and 0 virtual sites -56: -56: Total mass 391.552 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 114 atoms 8 residues -56: -56: Including chain 2 in system: 61 atoms 3 residues -56: -56: Including chain 3 in system: 83 atoms 5 residues -56: -56: Now there are 258 atoms and 16 residues -56: -56: Total mass in system 1882.146 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (1244 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 650 pairs -56: Before cleaning: 660 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Merged chains into joint molecule definitions at 3 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: Start terminus PHE-6: NH3+ -56: End terminus ILE-9: COO- -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 261 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 260, now 260 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 8 cmap torsion pairs -56: -56: There are 660 dihedrals, 45 impropers, 466 angles -56: 647 pairs, 260 bonds and 0 virtual sites -56: -56: Total mass 1900.162 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (253 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 123 pairs -56: Before cleaning: 123 dihedrals -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 6 donors and 4 acceptors were found. -56: There are 3 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 164 pairs -56: Before cleaning: 169 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 152 pairs -56: Before cleaning: 152 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 4 28 -56: -56: 2 'B' 4 33 -56: -56: 3 'B' 3 25 -56: -56: 4 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (28 atoms, 4 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue GLU5 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus GLU-5: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 51 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 50, now 50 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 123 dihedrals, 9 impropers, 88 angles -56: 123 pairs, 50 bonds and 0 virtual sites -56: -56: Total mass 434.421 a.m.u. -56: -56: Total charge -2.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (33 atoms, 4 residues) -56: -56: Identified residue PHE6 as a starting terminus. -56: -56: Identified residue ILE9 as a ending terminus. -56: Start terminus PHE-6: NH3+ -56: End terminus ILE-9: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 4 residues with 66 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 67, now 67 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2 cmap torsion pairs -56: -56: There are 169 dihedrals, 13 impropers, 118 angles -56: 161 pairs, 67 bonds and 0 virtual sites -56: -56: Total mass 472.547 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'B' (25 atoms, 3 residues) -56: -56: Identified residue LYS10 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus LYS-10: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 61 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 60, now 60 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 152 dihedrals, 5 impropers, 112 angles -56: 152 pairs, 60 bonds and 0 virtual sites -56: -56: Total mass 391.552 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Processing chain 4 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 51 atoms 4 residues -56: -56: Including chain 2 in system: 66 atoms 4 residues -56: -56: Including chain 3 in system: 61 atoms 3 residues -56: -56: Including chain 4 in system: 83 atoms 5 residues -56: -56: Now there are 261 atoms and 16 residues -56: -56: Total mass in system 1900.162 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (825 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 652 pairs -56: Before cleaning: 662 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: Merged chains into joint molecule definitions at 1 places. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 16 127 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (127 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus MET-12: COO- -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 256, now 256 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 12 cmap torsion pairs -56: -56: There are 662 dihedrals, 47 impropers, 460 angles -56: 649 pairs, 256 bonds and 0 virtual sites -56: -56: Total mass 1864.131 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (355 ms) -56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 14 donors and 15 acceptors were found. -56: There are 20 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 441 pairs -56: Before cleaning: 446 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 211 pairs -56: Before cleaning: 216 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 11 86 -56: -56: 2 'C' 5 41 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (86 atoms, 11 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue MET12 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus MET-12: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 11 residues with 172 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 173, now 173 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 9 cmap torsion pairs -56: -56: There are 446 dihedrals, 29 impropers, 312 angles -56: 438 pairs, 173 bonds and 0 virtual sites -56: -56: Total mass 1262.488 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'C' (41 atoms, 5 residues) -56: -56: Identified residue ASN13 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ASN-13: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 5 residues with 83 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 83, now 83 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 3 cmap torsion pairs -56: -56: There are 216 dihedrals, 18 impropers, 148 angles -56: 211 pairs, 83 bonds and 0 virtual sites -56: -56: Total mass 601.643 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 172 atoms 11 residues -56: -56: Including chain 2 in system: 83 atoms 5 residues -56: -56: Now there are 255 atoms and 16 residues -56: -56: Total mass in system 1864.131 a.m.u. -56: -56: Total charge in system 0.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (542 ms) -56: [----------] 8 tests from ChainSep/Pdb2gmxTest (3938 ms total) -56: -56: [----------] 4 tests from ChainChanges/Pdb2gmxTest -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on changing chain id only (ignoring TER records). -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (384 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records only (ignoring chain id). -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (310 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (102 ms) -56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 83 pairs -56: Before cleaning: 83 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 145 pairs -56: Before cleaning: 150 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -56: Read 'Fragments of peptides and ions', 47 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records and chain id changing. -56: -56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 3 19 -56: -56: 2 'B' 3 28 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (19 atoms, 3 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue ASP4 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus ASP-4: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 36 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 35, now 35 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 83 dihedrals, 6 impropers, 61 angles -56: 83 pairs, 35 bonds and 0 virtual sites -56: -56: Total mass 306.314 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'B' (28 atoms, 3 residues) -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue TRP20 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus TRP-20: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 3 residues with 57 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 58, now 58 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 1 cmap torsion pairs -56: -56: There are 150 dihedrals, 5 impropers, 103 angles -56: 142 pairs, 58 bonds and 0 virtual sites -56: -56: Total mass 404.468 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Writing topology -56: -56: Including chain 1 in system: 36 atoms 3 residues -56: -56: Including chain 2 in system: 57 atoms 3 residues -56: -56: Now there are 93 atoms and 6 residues -56: -56: Total mass in system 710.782 a.m.u. -56: -56: Total charge in system -1.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (129 ms) -56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (927 ms total) -56: -56: [----------] 4 tests from Cyclic/Pdb2gmxTest -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: WARNING: all CONECT records are ignored -56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 6040 pairs -56: Before cleaning: 6605 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 6040 pairs -56: Before cleaning: 6605 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -56: -56: Moved all the water blocks to the end -56: -56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms -56: -56: chain #res #atoms -56: -56: 1 'P' 71 1527 -56: -56: 2 'Q' 71 1527 -56: -56: 3 'Q' 7 7 -56: -56: 4 ' ' 10 10 (only water) -56: -56: 5 ' ' 16 16 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'P' (1527 atoms, 71 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 71 residues with 2297 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 2481, now 2481 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6605 dihedrals, 183 impropers, 4434 angles -56: 5827 pairs, 2481 bonds and 0 virtual sites -56: -56: Total mass 22984.514 a.m.u. -56: -56: Total charge -71.000 e -56: -56: Writing topology -56: -56: Processing chain 2 'Q' (1527 atoms, 71 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 71 residues with 2297 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: Number of bonds was 2481, now 2481 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 6605 dihedrals, 183 impropers, 4434 angles -56: 5827 pairs, 2481 bonds and 0 virtual sites -56: -56: Total mass 22984.514 a.m.u. -56: -56: Total charge -71.000 e -56: -56: Writing topology -56: -56: Processing chain 3 'Q' (7 atoms, 7 residues) -56: -56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -56: -56: Disabling further notes about ions. -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 7 residues with 7 atoms -56: Chain time... -56: -56: Making bonds... -56: -56: No bonds -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 0 angles -56: 0 pairs, 0 bonds and 0 virtual sites -56: -56: Total mass 170.135 a.m.u. -56: -56: Total charge 14.000 e -56: -56: Writing topology -56: -56: Processing chain 4 (10 atoms, 10 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 10 residues with 30 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 30, now 30 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 30 angles -56: 0 pairs, 30 bonds and 0 virtual sites -56: -56: Total mass 180.154 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Processing chain 5 (16 atoms, 16 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 48 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 48, now 48 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 48 angles -56: 0 pairs, 48 bonds and 0 virtual sites -56: -56: Total mass 288.246 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Including chain 1 in system: 2297 atoms 71 residues -56: -56: Including chain 2 in system: 2297 atoms 71 residues -56: -56: Including chain 3 in system: 7 atoms 7 residues -56: -56: Including chain 4 in system: 30 atoms 10 residues -56: -56: Including chain 5 in system: 48 atoms 16 residues -56: -56: Now there are 4679 atoms and 175 residues -56: -56: Total mass in system 46607.563 a.m.u. -56: -56: Total charge in system -128.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (838 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2325 pairs -56: Before cleaning: 2325 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -56: Read 'CARNOCYCLIN-A', 413 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 60 413 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (413 atoms, 60 residues) -56: -56: Identified residue LEU1 as a starting terminus. -56: -56: Identified residue LEU60 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 60 residues with 878 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 880, now 880 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 60 cmap torsion pairs -56: -56: There are 2325 dihedrals, 137 impropers, 1614 angles -56: 2319 pairs, 880 bonds and 0 virtual sites -56: -56: Total mass 5866.087 a.m.u. -56: -56: Total charge 4.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (162 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: WARNING: all CONECT records are ignored -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 12080 pairs -56: Before cleaning: 13210 dihedrals -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: Moved all the water blocks to the end -56: -56: Merged chains into joint molecule definitions at 2 places. -56: -56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms -56: -56: chain #res #atoms -56: -56: 1 'P' 149 3061 -56: -56: 2 ' ' 10 10 (only water) -56: -56: 3 ' ' 16 16 (only water) -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'P' (3061 atoms, 149 residues) -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Identified residue G1 as a starting terminus. -56: -56: Identified residue U71 as a ending terminus. -56: -56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -56: -56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -56: -56: Disabling further notes about ions. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 149 residues with 4601 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 4962, now 4962 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 13210 dihedrals, 366 impropers, 8868 angles -56: 11654 pairs, 4962 bonds and 0 virtual sites -56: -56: Total mass 46139.162 a.m.u. -56: -56: Total charge -128.000 e -56: -56: Writing topology -56: -56: Processing chain 2 (10 atoms, 10 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 10 residues with 30 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 30, now 30 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 30 angles -56: 0 pairs, 30 bonds and 0 virtual sites -56: -56: Total mass 180.154 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Processing chain 3 (16 atoms, 16 residues) -56: -56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 48 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 48, now 48 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 0 dihedrals, 0 impropers, 48 angles -56: 0 pairs, 48 bonds and 0 virtual sites -56: -56: Total mass 288.246 a.m.u. -56: -56: Total charge 0.000 e -56: -56: Including chain 1 in system: 4601 atoms 149 residues -56: -56: Including chain 2 in system: 30 atoms 10 residues -56: -56: Including chain 3 in system: 48 atoms 16 residues -56: -56: Now there are 4679 atoms and 175 residues -56: -56: Total mass in system 46607.563 a.m.u. -56: -56: Total charge in system -128.000 e -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (1326 ms) -56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -56: 9 out of 9 lines of specbond.dat converted successfully -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -56: Before cleaning: 2325 pairs -56: Before cleaning: 2325 dihedrals -56: Using the Charmm27 force field in directory charmm27.ff -56: -56: going to rename charmm27.ff/aminoacids.r2b -56: -56: going to rename charmm27.ff/rna.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -56: Read 'CARNOCYCLIN-A', 413 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 60 413 -56: -56: All occupancies are one -56: -56: Reading residue database... (Charmm27) -56: -56: Processing chain 1 'A' (413 atoms, 60 residues) -56: -56: Identified residue LEU1 as a starting terminus. -56: -56: Identified residue LEU60 as a ending terminus. -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 60 residues with 878 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 880, now 880 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 60 cmap torsion pairs -56: -56: There are 2325 dihedrals, 137 impropers, 1614 angles -56: 2319 pairs, 880 bonds and 0 virtual sites -56: -56: Total mass 5866.087 a.m.u. -56: -56: Total charge 4.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -56: -56: The Charmm27 force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (283 ms) -56: [----------] 4 tests from Cyclic/Pdb2gmxTest (2611 ms total) -56: -56: [----------] Global test environment tear-down -56: [==========] 39 tests from 6 test suites ran. (12214 ms total) -56: [ PASSED ] 39 tests. -56/92 Test #56: Pdb2gmx3Test .............................. Passed 12.23 sec -test 57 - Start 57: CorrelationsTest - -57: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" -57: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/correlationfunctions/tests -57: Test timeout computed to be: 30 -57: [==========] Running 21 tests from 3 test suites. -57: [----------] Global test environment set-up. -57: [----------] 10 tests from AutocorrTest -57: [ RUN ] AutocorrTest.EacNormal -57: [ OK ] AutocorrTest.EacNormal (31 ms) -57: [ RUN ] AutocorrTest.EacNoNormalize -57: [ OK ] AutocorrTest.EacNoNormalize (23 ms) -57: [ RUN ] AutocorrTest.EacCos -57: [ OK ] AutocorrTest.EacCos (40 ms) -57: [ RUN ] AutocorrTest.EacVector -57: [ OK ] AutocorrTest.EacVector (63 ms) -57: [ RUN ] AutocorrTest.EacRcross -57: [ OK ] AutocorrTest.EacRcross (1 ms) -57: [ RUN ] AutocorrTest.EacP0 -57: [ OK ] AutocorrTest.EacP0 (62 ms) -57: [ RUN ] AutocorrTest.EacP1 -57: [ OK ] AutocorrTest.EacP1 (120 ms) -57: [ RUN ] AutocorrTest.EacP2 -57: [ OK ] AutocorrTest.EacP2 (143 ms) -57: [ RUN ] AutocorrTest.EacP3 -57: [ OK ] AutocorrTest.EacP3 (2 ms) -57: [ RUN ] AutocorrTest.EacP4 -57: [ OK ] AutocorrTest.EacP4 (61 ms) -57: [----------] 10 tests from AutocorrTest (551 ms total) -57: -57: [----------] 10 tests from ExpfitTest -57: [ RUN ] ExpfitTest.EffnEXP1 -57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) -57: [ RUN ] ExpfitTest.EffnEXP2 -57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) -57: [ RUN ] ExpfitTest.EffnEXPEXP -57: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) -57: [ RUN ] ExpfitTest.EffnEXP5 -57: [ OK ] ExpfitTest.EffnEXP5 (2 ms) -57: [ RUN ] ExpfitTest.EffnEXP7 -57: [ OK ] ExpfitTest.EffnEXP7 (1 ms) -57: [ RUN ] ExpfitTest.EffnEXP9 -57: [ OK ] ExpfitTest.EffnEXP9 (8 ms) -57: [ RUN ] ExpfitTest.EffnERF -57: [ OK ] ExpfitTest.EffnERF (1 ms) -57: [ RUN ] ExpfitTest.EffnERREST -57: [ OK ] ExpfitTest.EffnERREST (1 ms) -57: [ RUN ] ExpfitTest.EffnVAC -57: [ OK ] ExpfitTest.EffnVAC (4 ms) -57: [ RUN ] ExpfitTest.EffnPRES -57: [ OK ] ExpfitTest.EffnPRES (8 ms) -57: [----------] 10 tests from ExpfitTest (29 ms total) -57: -57: [----------] 1 test from ManyAutocorrelationTest -57: [ RUN ] ManyAutocorrelationTest.Empty -57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) -57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) -57: -57: [----------] Global test environment tear-down -57: [==========] 21 tests from 3 test suites ran. (584 ms total) -57: [ PASSED ] 21 tests. -57/92 Test #57: CorrelationsTest .......................... Passed 0.60 sec -test 58 - Start 58: AnalysisDataUnitTests - -58: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" -58: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/analysisdata/tests -58: Test timeout computed to be: 30 -58: [==========] Running 69 tests from 14 test suites. -58: [----------] Global test environment set-up. -58: [----------] 3 tests from AnalysisDataInitializationTest -58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization -58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) -58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules -58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) -58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules -58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) -58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData -58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData -58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/1 (2 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData -58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) -58: -58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData -58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly -58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames -58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks -58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData -58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) -58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks -58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) -58: [----------] 8 tests from AnalysisDataCommonTest/3 (2 ms total) -58: -58: [----------] 4 tests from AnalysisArrayDataTest -58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly -58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) -58: [ RUN ] AnalysisArrayDataTest.StorageWorks -58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) -58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis -58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) -58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount -58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) -58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) -58: -58: [----------] 6 tests from AverageModuleTest -58: [ RUN ] AverageModuleTest.BasicTest -58: [ OK ] AverageModuleTest.BasicTest (0 ms) -58: [ RUN ] AverageModuleTest.HandlesMultipointData -58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) -58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets -58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging -58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) -58: [ RUN ] AverageModuleTest.CanCustomizeXAxis -58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) -58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis -58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) -58: [----------] 6 tests from AverageModuleTest (2 ms total) -58: -58: [----------] 2 tests from FrameAverageModuleTest -58: [ RUN ] FrameAverageModuleTest.BasicTest -58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) -58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets -58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 2 tests from FrameAverageModuleTest (0 ms total) -58: -58: [----------] 7 tests from AnalysisHistogramSettingsTest -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) -58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange -58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) -58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) -58: -58: [----------] 2 tests from SimpleHistogramModuleTest -58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly -58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) -58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll -58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -58: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) -58: -58: [----------] 3 tests from WeightedHistogramModuleTest -58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly -58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) -58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll -58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets -58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) -58: -58: [----------] 3 tests from BinAverageModuleTest -58: [ RUN ] BinAverageModuleTest.ComputesCorrectly -58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) -58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll -58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) -58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets -58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 3 tests from BinAverageModuleTest (1 ms total) -58: -58: [----------] 4 tests from AbstractAverageHistogramTest -58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly -58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram -58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth -58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) -58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins -58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) -58: [----------] 4 tests from AbstractAverageHistogramTest (2 ms total) -58: -58: [----------] 3 tests from LifetimeModuleTest -58: [ RUN ] LifetimeModuleTest.BasicTest -58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) -58: [ RUN ] LifetimeModuleTest.CumulativeTest -58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) -58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets -58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) -58: [----------] 3 tests from LifetimeModuleTest (1 ms total) -58: -58: [----------] Global test environment tear-down -58: [==========] 69 tests from 14 test suites ran. (20 ms total) -58: [ PASSED ] 69 tests. -58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.03 sec -test 59 - Start 59: CoordinateIOTests - -59: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" -59: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/coordinateio/tests -59: Test timeout computed to be: 30 -59: [==========] Running 67 tests from 20 test suites. -59: [----------] Global test environment set-up. -59: [----------] 1 test from OutputSelectorDeathTest -59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (2 ms) -59: [----------] 1 test from OutputSelectorDeathTest (2 ms total) -59: -59: [----------] 5 tests from TrajectoryFrameWriterTest -59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) -59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (2 ms) -59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks -59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) -59: [----------] 5 tests from TrajectoryFrameWriterTest (6 ms total) -59: -59: [----------] 5 tests from OutputAdapterContainer -59: [ RUN ] OutputAdapterContainer.MakeEmpty -59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) -59: [ RUN ] OutputAdapterContainer.AddAdapter -59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.RejectBadAdapter -59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter -59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) -59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters -59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) -59: [----------] 5 tests from OutputAdapterContainer (0 ms total) -59: -59: [----------] 3 tests from RegisterFrameConverterTest -59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks -59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) -59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks -59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) -59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees -59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) -59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) -59: -59: [----------] 5 tests from FlagTest -59: [ RUN ] FlagTest.CanSetSimpleFlag -59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) -59: [ RUN ] FlagTest.CanAddNewBox -59: [ OK ] FlagTest.CanAddNewBox (0 ms) -59: [ RUN ] FlagTest.SetsImplicitPrecisionChange -59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) -59: [ RUN ] FlagTest.SetsImplicitStartTimeChange -59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) -59: [ RUN ] FlagTest.SetsImplicitTimeStepChange -59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) -59: [----------] 5 tests from FlagTest (0 ms total) -59: -59: [----------] 5 tests from SetAtomsTest -59: [ RUN ] SetAtomsTest.RemovesExistingAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) -59: [ RUN ] SetAtomsTest.AddsNewAtoms -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) -59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) -59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) -59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) -59: [----------] 5 tests from SetAtomsTest (7 ms total) -59: -59: [----------] 2 tests from SetBothTimeTest -59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks -59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) -59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks -59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) -59: [----------] 2 tests from SetBothTimeTest (0 ms total) -59: -59: [----------] 2 tests from SetStartTimeTest -59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart -59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) -59: [ RUN ] SetStartTimeTest.WorksWithZeroStart -59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) -59: [----------] 2 tests from SetStartTimeTest (0 ms total) -59: -59: [----------] 1 test from SetTimeStepTest -59: [ RUN ] SetTimeStepTest.SetTimeStepWorks -59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) -59: [----------] 1 test from SetTimeStepTest (0 ms total) -59: -59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) -59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) -59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (8 ms total) -59: -59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) -59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (4 ms total) -59: -59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) -59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) -59: -59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) -59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (3 ms) -59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (11 ms total) -59: -59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) -59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (4 ms total) -59: -59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) -59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) -59: -59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles -59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) -59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) -59: -59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) -59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 -59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) -59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) -59: -59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles -59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) -59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) -59: -59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) -59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 -59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) -59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) -59: -59: [----------] 4 tests from ModuleSupported/NoOptionalOutput -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) -59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 -59: -59: WARNING: Masses and atomic (Van der Waals) radii will be guessed -59: based on residue and atom names, since they could not be -59: definitively assigned from the information in your input -59: files. These guessed numbers might deviate from the mass -59: and radius of the atom type. Please check the output -59: files if necessary. Note, that this functionality may -59: be removed in a future GROMACS version. Please, consider -59: using another file format for your input. -59: -59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) -59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) -59: -59: [----------] Global test environment tear-down -59: [==========] 67 tests from 20 test suites ran. (56 ms total) -59: [ PASSED ] 67 tests. -59/92 Test #59: CoordinateIOTests ......................... Passed 0.07 sec -test 60 - Start 60: TrajectoryAnalysisUnitTests - -60: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" -60: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests -60: Test timeout computed to be: 1920 -60: [==========] Running 393 tests from 21 test suites. -60: [----------] Global test environment set-up. -60: [----------] 11 tests from AngleModuleTest -60: [ RUN ] AngleModuleTest.ComputesSimpleAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesSimpleAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesDihedrals -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles -60: Reading frames from gro file 'Test system for different angles', 33 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) -60: [ RUN ] AngleModuleTest.ComputesMultipleAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) -60: [ RUN ] AngleModuleTest.HandlesDynamicSelections -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) -60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) -60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) -60: [----------] 11 tests from AngleModuleTest (16 ms total) -60: -60: [----------] 5 tests from ClustsizeTest -60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -60: There is one group in the index -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 24 -60: cmid: 2, cmax: 4, max_size: 6 -60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) -60: [ RUN ] ClustsizeTest.NoMolShortCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -60: There is one group in the index -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 24 -60: cmid: 1, cmax: 6, max_size: 6 -60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (12 ms) -60: [ RUN ] ClustsizeTest.MolDefaultCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 2, cmax: 4, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms) -60: [ RUN ] ClustsizeTest.MolShortCutoff -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 1, cmax: 6, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (2 ms) -60: [ RUN ] ClustsizeTest.MolCSize -60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Total number of atoms in clusters = 8 -60: cmid: 2, cmax: 4, max_size: 2 -60: 50%100%cmid: 2, cmax: 6, max_size: 2 -60: 50%100%[ OK ] ClustsizeTest.MolCSize (7 ms) -60: [----------] 5 tests from ClustsizeTest (38 ms total) -60: -60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory -60: Reading frames from gro file 'Test system', 8 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (1 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset -60: Reading frames from gro file 'Test system', 8 atoms. -60: Reading frame 0 time 0.000 -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) -60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory -60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) -60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) -60: -60: [----------] 4 tests from ConvertTrjModuleTest -60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (6 ms) -60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (9 ms) -60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) -60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -60: Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (0 ms) -60: [----------] 4 tests from ConvertTrjModuleTest (18 ms total) -60: -60: [----------] 6 tests from DistanceModuleTest -60: [ RUN ] DistanceModuleTest.ComputesDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2: -60: Number of samples: 5 -60: Average distance: 1.43246 nm -60: Standard deviation: 0.96700 nm -60: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) -60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2: -60: Number of samples: 5 -60: Average distance: 1.43246 nm -60: Standard deviation: 0.96700 nm -60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: -60: Number of samples: 4 -60: Average distance: 1.81066 nm -60: Standard deviation: 0.79289 nm -60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) -60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: atomname S1 S2 and res_cog x < 2.8: -60: Number of samples: 3 -60: Average distance: 1.72076 nm -60: Standard deviation: 1.24839 nm -60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: Contacts: -60: Number of samples: 2 -60: Average distance: 1.00000 nm -60: Standard deviation: 0.00000 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: SuccessiveContacts: -60: Number of samples: 2 -60: Average distance: 1.00000 nm -60: Standard deviation: 0.00000 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) -60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: ManyContacts: -60: Number of samples: 10 -60: Average distance: 1.82913 nm -60: Standard deviation: 0.78478 nm -60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) -60: [----------] 6 tests from DistanceModuleTest (15 ms total) -60: -60: [----------] 2 tests from ExtractClusterModuleTest -60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms -60: trr version: GMX_trn_file (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -60: Analyzed 26 frames, last time 0.050 -60: There are 8 clusters containing 26 structures, highest framenr is 25 -60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (5 ms) -60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset -60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -60: Analyzed 26 frames, last time 0.050 -60: There are 8 clusters containing 26 structures, highest framenr is 25 -60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (5 ms) -60: [----------] 2 tests from ExtractClusterModuleTest (10 ms total) -60: -60: [----------] 2 tests from FreeVolumeModuleTest -60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for CO2-RM. Set to zero. -60: Could not determine VDW radius for 40 particles. These were set to zero. -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: cutoff = 0.18 nm -60: probe_radius = 0 nm -60: seed = 13 -60: ninsert = 1000 probes per nm^3 -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -60: Spoel, Luciano T. Costa -60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -60: Environ. Sci. Technol. (2013) -60: DOI: 10.1021/es4020986 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Free volume 38.02 +/- 0.00 % -60: Total volume 68.92 +/- 0.00 nm^3 -60: Number of molecules 340 total mass 63491.38 Dalton -60: Average molar mass: 186.74 Dalton -60: Density rho: 1529.71 +/- 0.00 nm^3 -60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 -60: Fractional free volume 0.194 +/- 0.000 -60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (48 ms) -60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: cutoff = 0.18 nm -60: probe_radius = 0 nm -60: seed = 17 -60: ninsert = 1000 probes per nm^3 -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -60: Spoel, Luciano T. Costa -60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -60: Environ. Sci. Technol. (2013) -60: DOI: 10.1021/es4020986 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Free volume 38.48 +/- 0.00 % -60: Total volume 68.92 +/- 0.00 nm^3 -60: Number of molecules 340 total mass 63491.38 Dalton -60: Average molar mass: 186.74 Dalton -60: Density rho: 1529.71 +/- 0.00 nm^3 -60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 -60: Fractional free volume 0.200 +/- 0.000 -60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (49 ms) -60: [----------] 2 tests from FreeVolumeModuleTest (98 ms total) -60: -60: [----------] 13 tests from MsdModuleTest -60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) -60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) -60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (7 ms) -60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau -60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -60: Analyzed 10 frames, last time 9.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) -60: [ RUN ] MsdModuleTest.multipleGroupsWork -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to 125687211 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.multipleGroupsWork (32 ms) -60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 -60: Analyzed 21 frames, last time 2.000 -60: Setting the LD random seed to 519028095 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (21 ms) -60: [ RUN ] MsdModuleTest.trestartLessThanDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 1945698109 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartLessThanDt (18 ms) -60: [ RUN ] MsdModuleTest.trestartGreaterThanDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -270639661 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartGreaterThanDt (133 ms) -60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1678311683 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (13 ms) -60: [ RUN ] MsdModuleTest.molTest -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -959709582 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.molTest (16 ms) -60: [ RUN ] MsdModuleTest.beginFit -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -45146 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.beginFit (17 ms) -60: [ RUN ] MsdModuleTest.endFit -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -547621393 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.endFit (17 ms) -60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -60: For energy conservation with LINCS, lincs_iter should be 2 or larger. -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 1818.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: NVE simulation: will use the initial temperature of 288.764 K for -60: determining the Verlet buffer size -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: There are 9 non-linear virtual site constructions. Their contribution to -60: the energy error is approximated. In most cases this does not affect the -60: error significantly. -60: -60: -60: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 5 NOTEs -60: NOTE: You provided an index file -60: /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx -60: (with -n), but it was not used by any selection. -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -60: Analyzed 21 frames, last time 40.000 -60: Setting the LD random seed to -201621646 -60: -60: Generated 2145 of the 2145 non-bonded parameter combinations -60: -60: Generated 2145 of the 2145 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -60: -60: Excluding 2 bonded neighbours molecule type 'SOL' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -60: -60: Cleaning up constraints and constant bonded interactions with virtual sites -60: -60: Converted 15 Bonds with virtual sites to connections, 7 left -60: -60: Removed 18 Angles with virtual sites, 21 left -60: -60: Removed 10 Proper Dih.s with virtual sites, 44 left -60: -60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -60: -60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -60: -60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -60: -60: Note that mdrun will redetermine rlist based on the actual pair-list setup -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (58 ms) -60: [----------] 13 tests from MsdModuleTest (341 ms total) -60: -60: [----------] 9 tests from PairDistanceModuleTest -60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (5 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) -60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (11 ms) -60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) -60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) -60: [----------] 9 tests from PairDistanceModuleTest (33 ms total) -60: -60: [----------] 5 tests from RdfModuleTest -60: [ RUN ] RdfModuleTest.BasicTest -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.BasicTest (22 ms) -60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork -60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. -60: Reading frame 0 time 0.000 Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (10 ms) -60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (11 ms) -60: [ RUN ] RdfModuleTest.CalculatesSurf -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.CalculatesSurf (6 ms) -60: [ RUN ] RdfModuleTest.CalculatesXY -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] RdfModuleTest.CalculatesXY (16 ms) -60: [----------] 5 tests from RdfModuleTest (67 ms total) -60: -60: [----------] 5 tests from SasaModuleTest -60: [ RUN ] SasaModuleTest.BasicTest -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.BasicTest (6 ms) -60: [ RUN ] SasaModuleTest.HandlesSelectedResidues -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesSelectedResidues (5 ms) -60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) -60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) -60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -60: of Surface Area and Volume and to Dot Surface Contouring of Molecular -60: Assemblies -60: J. Comp. Chem. (1995) -60: DOI: 10.1002/jcc.540160303 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -60: from the source below. This means the results may be different -60: compared to previous GROMACS versions. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. Bondi -60: van der Waals Volumes and Radii -60: J. Phys. Chem. (1964) -60: DOI: 10.1021/j100785a001 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Analyzed topology coordinates -60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) -60: [----------] 5 tests from SasaModuleTest (23 ms total) -60: -60: [----------] 8 tests from SelectModuleTest -60: [ RUN ] SelectModuleTest.BasicTest -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.BasicTest (2 ms) -60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) -60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (9 ms) -60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) -60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) -60: [ RUN ] SelectModuleTest.NormalizesSizes -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) -60: [ RUN ] SelectModuleTest.WritesResidueNumbers -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) -60: [ RUN ] SelectModuleTest.WritesResidueIndices -60: Analyzed topology coordinates -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) -60: [----------] 8 tests from SelectModuleTest (19 ms total) -60: -60: [----------] 10 tests from SurfaceAreaTest -60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint -60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) -60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints -60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) -60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius -60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints12 -60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints32 -60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints42 -60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) -60: [ RUN ] SurfaceAreaTest.SurfacePoints122 -60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) -60: [ RUN ] SurfaceAreaTest.Computes100Points -60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) -60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC -60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) -60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC -60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) -60: [----------] 10 tests from SurfaceAreaTest (5 ms total) -60: -60: [----------] 4 tests from TopologyInformation -60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile -60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) -60: [ RUN ] TopologyInformation.WorksWithGroFile -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) -60: [ RUN ] TopologyInformation.WorksWithPdbFile -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) -60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile -60: -60: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: For a correct single-point energy evaluation with nsteps = 0, use -60: continuation = yes to avoid constraining the input coordinates. -60: -60: Generating 1-4 interactions: fudge = 0.5 -60: -60: NOTE 2 [file lysozyme.top, line 1465]: -60: System has non-zero total charge: 2.000000 -60: Total charge should normally be an integer. See -60: https://manual.gromacs.org/current/user-guide/floating-point.html -60: for discussion on how close it should be to an integer. -60: -60: -60: -60: Number of degrees of freedom in T-Coupling group rest is 465.00 -60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -60: -60: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: NVE simulation with an initial temperature of zero: will use a Verlet -60: buffer of 10%. Check your energy drift! -60: -60: -60: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -60: You are using a plain Coulomb cut-off, which might produce artifacts. -60: You might want to consider using PME electrostatics. -60: -60: -60: -60: There were 4 NOTEs -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -60: Setting the LD random seed to 1979375596 -60: -60: Generated 330891 of the 330891 non-bonded parameter combinations -60: -60: Generated 330891 of the 330891 1-4 parameter combinations -60: -60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -60: -60: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -60: Analysing residue names: -60: There are: 10 Protein residues -60: Analysing Protein... -60: -60: This run will generate roughly 0 Mb of data -60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (291 ms) -60: [----------] 4 tests from TopologyInformation (293 ms total) -60: -60: [----------] 4 tests from TrajectoryModuleTest -60: [ RUN ] TrajectoryModuleTest.BasicTest -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) -60: [ RUN ] TrajectoryModuleTest.PlotsXOnly -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) -60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) -60: [ RUN ] TrajectoryModuleTest.HandlesNoForces -60: Reading frames from gro file 'Test system', 15 atoms. -60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -60: Analyzed 2 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: [ OK ] TrajectoryModuleTest.HandlesNoForces (2 ms) -60: [----------] 4 tests from TrajectoryModuleTest (6 ms total) -60: -60: [----------] 5 tests from UnionFinderTest -60: [ RUN ] UnionFinderTest.WorksEmpty -60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) -60: [ RUN ] UnionFinderTest.BasicMerges -60: [ OK ] UnionFinderTest.BasicMerges (0 ms) -60: [ RUN ] UnionFinderTest.LargerMerges -60: [ OK ] UnionFinderTest.LargerMerges (0 ms) -60: [ RUN ] UnionFinderTest.LongRightMerge -60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) -60: [ RUN ] UnionFinderTest.LongLeftMerge -60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) -60: [----------] 5 tests from UnionFinderTest (0 ms total) -60: -60: [----------] 1 test from MappedUnionFinderTest -60: [ RUN ] MappedUnionFinderTest.BasicMerges -60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) -60: [----------] 1 test from MappedUnionFinderTest (0 ms total) -60: -60: [----------] 192 tests from MoleculeTests/DsspModuleTest -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (17 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (17 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (22 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (21 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (18 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (28 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (34 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (25 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (17 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (23 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (35 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (21 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (53 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (32 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (38 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (31 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (86 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (45 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (71 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (32 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (23 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (23 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (20 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (22 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (14 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (34 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (30 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (26 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (19 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (15 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (16 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (11 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (18 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (13 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (12 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (21 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (31 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (9 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (10 ms) -60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 -60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -60: Last frame 0 time 500.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: W. Kabsch, C. Sander -60: Dictionary of protein secondary structure: pattern recognition of -60: hydrogen-bonded and geometrical features -60: Biopolymers (1983) -60: DOI: 10.1002/bip.360221211 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -60: Trajectories -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c01344 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (9 ms) -60: [----------] 192 tests from MoleculeTests/DsspModuleTest (3017 ms total) -60: -60: [----------] 3 tests from GyrateTests/GyrateModuleTest -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) -60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (18 ms) -60: [----------] 3 tests from GyrateTests/GyrateModuleTest (27 ms total) -60: -60: [----------] 96 tests from HBondTests/HbondModuleTest -60: [ RUN ] HBondTests/HbondModuleTest.Works/0 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/0 (28 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/1 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/1 (14 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/2 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/2 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/3 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/3 (15 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/4 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/4 (17 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/5 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/5 (33 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/6 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/6 (20 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/7 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/7 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/8 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/8 (25 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/9 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/9 (14 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/10 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/10 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/11 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/11 (13 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/12 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/12 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/13 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/13 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/14 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/14 (18 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/15 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/15 (8 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/16 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/16 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/17 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/17 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/18 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/18 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/19 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/19 (18 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/20 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/20 (21 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/21 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/21 (26 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/22 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/22 (10 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/23 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/23 (9 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/24 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/24 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/25 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/25 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/26 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/26 (6 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/27 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/27 (6 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/28 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/28 (12 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/29 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/29 (14 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/30 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/30 (7 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/31 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/31 (6 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/32 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/32 (50 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/33 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/33 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/34 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/34 (45 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/35 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/35 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/36 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/36 (40 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/37 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/37 (33 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/38 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/38 (42 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/39 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/39 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/40 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/40 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/41 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/41 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/42 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/42 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/43 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/43 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/44 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/44 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/45 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/45 (116 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/46 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/46 (44 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/47 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/47 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/48 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/48 (44 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/49 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/49 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/50 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/50 (32 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/51 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/51 (31 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/52 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/52 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/53 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/53 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/54 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/54 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/55 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/55 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/56 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/56 (98 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/57 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/57 (32 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/58 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/58 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/59 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/59 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/60 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/60 (42 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/61 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 27 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/61 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/62 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 56 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/62 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/63 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -60: Selection 'Protein' has 29 acceptors and 4 donors. -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: Merging hbonds with Acceptor and Donor swapped -60: [ OK ] HBondTests/HbondModuleTest.Works/63 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/64 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/64 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/65 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/65 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/66 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/66 (47 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/67 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/67 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/68 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/68 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/69 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/69 (42 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/70 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/70 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/71 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/71 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/72 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/72 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/73 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/73 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/74 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/74 (43 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/75 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/75 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/76 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/76 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/77 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/77 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/78 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/78 (40 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/79 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/79 (36 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/80 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/80 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/81 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/81 (34 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/82 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/82 (40 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/83 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/83 (39 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/84 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/84 (35 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/85 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/85 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/86 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/86 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/87 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/87 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/88 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/88 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/89 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/89 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/90 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/90 (66 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/91 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/91 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/92 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/92 (41 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/93 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/93 (38 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/94 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/94 (37 ms) -60: [ RUN ] HBondTests/HbondModuleTest.Works/95 -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -60: Analyzed 2 frames, last time 10.000 -60: -60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -60: Selection 'Water' has 1160 acceptors and 1160 donors. -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -60: Memory Limitation -60: Journal of Chemical Information and Modeling (2024) -60: DOI: 10.1021/acs.jcim.3c02087 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] HBondTests/HbondModuleTest.Works/95 (37 ms) -60: [----------] 96 tests from HBondTests/HbondModuleTest (3367 ms total) -60: -60: [----------] 4 tests from MoleculeTests/ScatteringModule -60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: D. T. Cromer, J. B. Mann -60: X-ray scattering factors computed from numerical Hartree-Fock wave functions -60: Acta Cryst. A (1968) -60: DOI: 10.1107/S0567739468000550 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (201 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (12 ms) -60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 -60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -60: Last frame 0 time 0.000 -60: Analyzed 1 frames, last time 0.000 -60: -60: WARNING: Masses and atomic (Van der Waals) radii will be guessed -60: based on residue and atom names, since they could not be -60: definitively assigned from the information in your input -60: files. These guessed numbers might deviate from the mass -60: and radius of the atom type. Please check the output -60: files if necessary. Note, that this functionality may -60: be removed in a future GROMACS version. Please, consider -60: using another file format for your input. -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -60: Method for calculating small-angle neutron scattering spectra using all-atom -60: molecular dynamics trajectories -60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -60: DOI: 10.1134/S1027451013060372 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: -60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -60: D. T. Cromer, J. B. Mann -60: X-ray scattering factors computed from numerical Hartree-Fock wave functions -60: Acta Cryst. A (1968) -60: DOI: 10.1107/S0567739468000550 -60: -------- -------- --- Thank You --- -------- -------- -60: -60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (45 ms) -60: [----------] 4 tests from MoleculeTests/ScatteringModule (268 ms total) -60: -60: [----------] Global test environment tear-down -60: [==========] 393 tests from 21 test suites ran. (7673 ms total) -60: [ PASSED ] 393 tests. -60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 7.70 sec -test 61 - Start 61: EnergyAnalysisUnitTests - -61: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" -61: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis/tests -61: Test timeout computed to be: 30 -61: [==========] Running 12 tests from 5 test suites. -61: [----------] Global test environment set-up. -61: [----------] 2 tests from EnergyTermTest -61: [ RUN ] EnergyTermTest.ConstructWorks -61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) -61: [ RUN ] EnergyTermTest.AddFrameWorks -61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) -61: [----------] 2 tests from EnergyTermTest (0 ms total) -61: -61: [----------] 1 test from DhdlTest -61: [ RUN ] DhdlTest.ExtractDhdl -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file -61: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) -61: Note: file tpx version 110, software tpx version 137 -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 -61: -61: -61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg -61: [ OK ] DhdlTest.ExtractDhdl (15 ms) -61: [----------] 1 test from DhdlTest (15 ms total) -61: -61: [----------] 1 test from OriresTest -61: [ RUN ] OriresTest.ExtractOrires -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file -61: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) -61: Note: file tpx version 111, software tpx version 137 -61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) -61: End your selection with 0 -61: Selecting all 7 orientation restraints -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 -61: [ OK ] OriresTest.ExtractOrires (10 ms) -61: [----------] 1 test from OriresTest (10 ms total) -61: -61: [----------] 5 tests from EnergyTest -61: [ RUN ] EnergyTest.ExtractEnergy -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) -61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -61: [ OK ] EnergyTest.ExtractEnergy (1 ms) -61: [ RUN ] EnergyTest.ExtractEnergyByNumber -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) -61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -61: Pres. DC -268.49 3 8.52175 13.2804 (bar) -61: [ OK ] EnergyTest.ExtractEnergyByNumber (2 ms) -61: [ RUN ] EnergyTest.ExtractEnergyMixed -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -61: 13 Box-Z 14 Volume 15 Density 16 pV -61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: [ OK ] EnergyTest.ExtractEnergyMixed (3 ms) -61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -61: 37 1/Viscosity 38 T-System 39 Lamb-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -61: -61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets -61: All statistics are over 3 points (frames) -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) -61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -61: -61: Select the terms you want from the following list by -61: selecting either (part of) the name or the number or a combination. -61: End your selection with an empty line or a zero. -61: ------------------------------------------------------------------- -61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -61: 37 1/Viscosity 38 T-System 39 Lamb-System -61: -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -61: -61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets -61: All statistics are over 3 points (frames) -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) -61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) -61: [----------] 5 tests from EnergyTest (9 ms total) -61: -61: [----------] 3 tests from ViscosityTest -61: [ RUN ] ViscosityTest.EinsteinViscosity -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosity (47 ms) -61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (72 ms) -61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments -61: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -61: -61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -61: All statistics are over 5001 points -61: -61: Energy Average Err.Est. RMSD Tot-Drift -61: ------------------------------------------------------------------------------- -61: Pres-XX 20.2092 65 717.193 185.978 (bar) -61: Pres-XY -47.7351 39 372.522 207.456 (bar) -61: Pres-XZ 11.477 31 379.79 6.80818 (bar) -61: Pres-YX -47.7106 39 372.525 207.5 (bar) -61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -61: Pres-YZ -41.3534 45 401.216 114.663 (bar) -61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -61: Pres-ZY -41.3119 45 401.196 114.743 (bar) -61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -61: -61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (55 ms) -61: [----------] 3 tests from ViscosityTest (176 ms total) -61: -61: [----------] Global test environment tear-down -61: [==========] 12 tests from 5 test suites ran. (210 ms total) -61: [ PASSED ] 12 tests. -61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.22 sec -test 62 - Start 62: ToolUnitTests - -62: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" -62: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests -62: Test timeout computed to be: 1920 -62: [==========] Running 63 tests from 8 test suites. -62: [----------] Global test environment set-up. -62: [----------] 2 tests from DumpTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Setting the LD random seed to 1996154861 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ RUN ] DumpTest.WorksWithTpr -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: -62: inputrec: -62: integrator = md -62: tinit = 0 -62: dt = 0.001 -62: nsteps = 0 -62: init-step = 0 -62: simulation-part = 1 -62: mts = false -62: mass-repartition-factor = 1 -62: comm-mode = Linear -62: nstcomm = 100 -62: bd-fric = 0 -62: ld-seed = 1996154861 -62: emtol = 10 -62: emstep = 0.01 -62: niter = 20 -62: fcstep = 0 -62: nstcgsteep = 1000 -62: nbfgscorr = 10 -62: rtpi = 0.05 -62: nstxout = 0 -62: nstvout = 0 -62: nstfout = 0 -62: nstlog = 1000 -62: nstcalcenergy = 100 -62: nstenergy = 1000 -62: nstxout-compressed = 0 -62: compressed-x-precision = 1000 -62: cutoff-scheme = Verlet -62: nstlist = 10 -62: pbc = xyz -62: periodic-molecules = false -62: verlet-buffer-tolerance = -1 -62: verlet-buffer-pressure-tolerance = 0.5 -62: rlist = 1.1 -62: coulombtype = Cut-off -62: coulomb-modifier = Potential-shift -62: rcoulomb-switch = 0 -62: rcoulomb = 1 -62: epsilon-r = 1 -62: epsilon-rf = inf -62: vdw-type = Cut-off -62: vdw-modifier = Potential-shift -62: rvdw-switch = 0 -62: rvdw = 1 -62: DispCorr = No -62: table-extension = 1 -62: fourierspacing = 0.12 -62: fourier-nx = 0 -62: fourier-ny = 0 -62: fourier-nz = 0 -62: pme-order = 4 -62: ewald-rtol = 1e-05 -62: ewald-rtol-lj = 0.001 -62: lj-pme-comb-rule = Geometric -62: ewald-geometry = 3d -62: epsilon-surface = 0 -62: ensemble-temperature-setting = not available -62: tcoupl = No -62: nsttcouple = -1 -62: nh-chain-length = 0 -62: print-nose-hoover-chain-variables = false -62: pcoupl = No -62: refcoord-scaling = No -62: posres-com: not available -62: posres-comB: not available -62: QMMM = false -62: qm-opts: -62: ngQM = 0 -62: constraint-algorithm = Lincs -62: continuation = false -62: Shake-SOR = false -62: shake-tol = 0.0001 -62: lincs-order = 4 -62: lincs-iter = 1 -62: lincs-warnangle = 30 -62: nwall = 0 -62: wall-type = 9-3 -62: wall-r-linpot = -1 -62: wall-atomtype[0] = -1 -62: wall-atomtype[1] = -1 -62: wall-density[0] = 0 -62: wall-density[1] = 0 -62: wall-ewald-zfac = 3 -62: pull = false -62: awh = false -62: rotation = false -62: interactiveMD = false -62: disre = No -62: disre-weighting = Conservative -62: disre-mixed = false -62: dr-fc = 1000 -62: dr-tau = 0 -62: nstdisreout = 100 -62: orire-fc = 0 -62: orire-tau = 0 -62: nstorireout = 100 -62: free-energy = no -62: cos-acceleration = 0 -62: deform (3x3): -62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: simulated-tempering = false -62: swapcoords = no -62: userint1 = 0 -62: userint2 = 0 -62: userint3 = 0 -62: userint4 = 0 -62: userreal1 = 0 -62: userreal2 = 0 -62: userreal3 = 0 -62: userreal4 = 0 -62: applied-forces: -62: electric-field: -62: x: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: y: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: z: -62: E0 = 0 -62: omega = 0 -62: t0 = 0 -62: sigma = 0 -62: density-guided-simulation: -62: active = false -62: group = protein -62: similarity-measure = inner-product -62: atom-spreading-weight = unity -62: force-constant = 1e+09 -62: gaussian-transform-spreading-width = 0.2 -62: gaussian-transform-spreading-range-in-multiples-of-width = 4 -62: reference-density-filename = reference.mrc -62: nst = 1 -62: normalize-densities = true -62: adaptive-force-scaling = false -62: adaptive-force-scaling-time-constant = 4 -62: shift-vector = -62: transformation-matrix = -62: qmmm-cp2k: -62: active = false -62: qmgroup = System -62: qmmethod = PBE -62: qmfilenames = -62: qmcharge = 0 -62: qmmultiplicity = 1 -62: colvars: -62: active = false -62: configfile = -62: seed = -1 -62: nnpot: -62: active = false -62: modelfile = model.pt -62: input-group = System -62: model-input1 = -62: model-input2 = -62: model-input3 = -62: model-input4 = -62: grpopts: -62: nrdf: 465 -62: ref-t: 0 -62: tau-t: 0 -62: annealing: No -62: annealing-npoints: 0 -62: acc: 0 0 0 -62: nfreeze: N N N -62: energygrp-flags[ 0]: 0 -62: header: -62: bIr = present -62: bBox = present -62: bTop = present -62: bX = present -62: bV = present -62: bF = not present -62: natoms = 156 -62: lambda = 0.000000e+00 -62: buffer size = 57082 -62: topology: -62: name="First 10 residues from 1AKI" -62: #atoms = 156 -62: #molblock = 1 -62: molblock (0): -62: moltype = 0 "Protein_chain_B" -62: #molecules = 1 -62: #posres_xA = 0 -62: #posres_xB = 0 -62: bIntermolecularInteractions = false -62: ffparams: -62: atnr=10 -62: ntypes=212 -62: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 -62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 -62: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 -62: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 -62: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 -62: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 -62: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 -62: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 -62: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 -62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 -62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 -62: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 -62: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 -62: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 -62: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 -62: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 -62: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 -62: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 -62: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 -62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 -62: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 -62: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 -62: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 -62: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 -62: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 -62: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 -62: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 -62: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 -62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 -62: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 -62: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 -62: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 -62: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 -62: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 -62: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 -62: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 -62: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 -62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 -62: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 -62: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 -62: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 -62: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 -62: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 -62: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 -62: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 -62: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 -62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 -62: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 -62: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 -62: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 -62: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 -62: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 -62: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 -62: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 -62: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 -62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 -62: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 -62: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 -62: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 -62: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 -62: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 -62: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 -62: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 -62: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 -62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 -62: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 -62: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 -62: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 -62: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 -62: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 -62: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 -62: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 -62: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 -62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -62: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 -62: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 -62: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 -62: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 -62: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 -62: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 -62: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 -62: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 -62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 -62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 -62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 -62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 -62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 -62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 -62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 -62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 -62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 -62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 -62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 -62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 -62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 -62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 -62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 -62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 -62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 -62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 -62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 -62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 -62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 -62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 -62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 -62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 -62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 -62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 -62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 -62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 -62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 -62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 -62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 -62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 -62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 -62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 -62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 -62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 -62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 -62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 -62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 -62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 -62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 -62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 -62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 -62: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -62: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -62: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 -62: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 -62: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 -62: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 -62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 -62: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 -62: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 -62: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 -62: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 -62: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 -62: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 -62: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 -62: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 -62: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 -62: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 -62: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 -62: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 -62: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 -62: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 -62: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 -62: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 -62: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 -62: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 -62: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 -62: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 -62: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 -62: reppow = 12 -62: fudgeQQ = 0.5 -62: cmap -62: moltype (0): -62: name="Protein_chain_B" -62: atoms: -62: atom (156): -62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} -62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} -62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} -62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} -62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} -62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} -62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} -62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} -62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} -62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} -62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} -62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} -62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} -62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} -62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} -62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} -62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} -62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} -62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} -62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} -62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} -62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} -62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} -62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} -62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} -62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} -62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} -62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} -62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} -62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} -62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} -62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} -62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} -62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} -62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} -62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} -62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} -62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} -62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} -62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} -62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} -62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} -62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} -62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} -62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} -62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} -62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} -62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} -62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} -62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} -62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} -62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} -62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} -62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} -62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} -62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} -62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} -62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} -62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} -62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} -62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} -62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} -62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} -62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} -62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} -62: atom (156): -62: atom[0]={name="N"} -62: atom[1]={name="H1"} -62: atom[2]={name="H2"} -62: atom[3]={name="H3"} -62: atom[4]={name="CA"} -62: atom[5]={name="HA"} -62: atom[6]={name="CB"} -62: atom[7]={name="HB1"} -62: atom[8]={name="HB2"} -62: atom[9]={name="CG"} -62: atom[10]={name="HG1"} -62: atom[11]={name="HG2"} -62: atom[12]={name="CD"} -62: atom[13]={name="HD1"} -62: atom[14]={name="HD2"} -62: atom[15]={name="CE"} -62: atom[16]={name="HE1"} -62: atom[17]={name="HE2"} -62: atom[18]={name="NZ"} -62: atom[19]={name="HZ1"} -62: atom[20]={name="HZ2"} -62: atom[21]={name="HZ3"} -62: atom[22]={name="C"} -62: atom[23]={name="O"} -62: atom[24]={name="N"} -62: atom[25]={name="H"} -62: atom[26]={name="CA"} -62: atom[27]={name="HA"} -62: atom[28]={name="CB"} -62: atom[29]={name="HB"} -62: atom[30]={name="CG1"} -62: atom[31]={name="HG11"} -62: atom[32]={name="HG12"} -62: atom[33]={name="HG13"} -62: atom[34]={name="CG2"} -62: atom[35]={name="HG21"} -62: atom[36]={name="HG22"} -62: atom[37]={name="HG23"} -62: atom[38]={name="C"} -62: atom[39]={name="O"} -62: atom[40]={name="N"} -62: atom[41]={name="H"} -62: atom[42]={name="CA"} -62: atom[43]={name="HA"} -62: atom[44]={name="CB"} -62: atom[45]={name="HB1"} -62: atom[46]={name="HB2"} -62: atom[47]={name="CG"} -62: atom[48]={name="CD1"} -62: atom[49]={name="HD1"} -62: atom[50]={name="CD2"} -62: atom[51]={name="HD2"} -62: atom[52]={name="CE1"} -62: atom[53]={name="HE1"} -62: atom[54]={name="CE2"} -62: atom[55]={name="HE2"} -62: atom[56]={name="CZ"} -62: atom[57]={name="HZ"} -62: atom[58]={name="C"} -62: atom[59]={name="O"} -62: atom[60]={name="N"} -62: atom[61]={name="H"} -62: atom[62]={name="CA"} -62: atom[63]={name="HA1"} -62: atom[64]={name="HA2"} -62: atom[65]={name="C"} -62: atom[66]={name="O"} -62: atom[67]={name="N"} -62: atom[68]={name="H"} -62: atom[69]={name="CA"} -62: atom[70]={name="HA"} -62: atom[71]={name="CB"} -62: atom[72]={name="HB1"} -62: atom[73]={name="HB2"} -62: atom[74]={name="CG"} -62: atom[75]={name="HG1"} -62: atom[76]={name="HG2"} -62: atom[77]={name="CD"} -62: atom[78]={name="HD1"} -62: atom[79]={name="HD2"} -62: atom[80]={name="NE"} -62: atom[81]={name="HE"} -62: atom[82]={name="CZ"} -62: atom[83]={name="NH1"} -62: atom[84]={name="HH11"} -62: atom[85]={name="HH12"} -62: atom[86]={name="NH2"} -62: atom[87]={name="HH21"} -62: atom[88]={name="HH22"} -62: atom[89]={name="C"} -62: atom[90]={name="O"} -62: atom[91]={name="N"} -62: atom[92]={name="H"} -62: atom[93]={name="CA"} -62: atom[94]={name="HA"} -62: atom[95]={name="CB"} -62: atom[96]={name="HB1"} -62: atom[97]={name="HB2"} -62: atom[98]={name="SG"} -62: atom[99]={name="HG"} -62: atom[100]={name="C"} -62: atom[101]={name="O"} -62: atom[102]={name="N"} -62: atom[103]={name="H"} -62: atom[104]={name="CA"} -62: atom[105]={name="HA"} -62: atom[106]={name="CB"} -62: atom[107]={name="HB1"} -62: atom[108]={name="HB2"} -62: atom[109]={name="CG"} -62: atom[110]={name="HG1"} -62: atom[111]={name="HG2"} -62: atom[112]={name="CD"} -62: atom[113]={name="OE1"} -62: atom[114]={name="OE2"} -62: atom[115]={name="C"} -62: atom[116]={name="O"} -62: atom[117]={name="N"} -62: atom[118]={name="H"} -62: atom[119]={name="CA"} -62: atom[120]={name="HA"} -62: atom[121]={name="CB"} -62: atom[122]={name="HB1"} -62: atom[123]={name="HB2"} -62: atom[124]={name="CG"} -62: atom[125]={name="HG"} -62: atom[126]={name="CD1"} -62: atom[127]={name="HD11"} -62: atom[128]={name="HD12"} -62: atom[129]={name="HD13"} -62: atom[130]={name="CD2"} -62: atom[131]={name="HD21"} -62: atom[132]={name="HD22"} -62: atom[133]={name="HD23"} -62: atom[134]={name="C"} -62: atom[135]={name="O"} -62: atom[136]={name="N"} -62: atom[137]={name="H"} -62: atom[138]={name="CA"} -62: atom[139]={name="HA"} -62: atom[140]={name="CB"} -62: atom[141]={name="HB1"} -62: atom[142]={name="HB2"} -62: atom[143]={name="HB3"} -62: atom[144]={name="C"} -62: atom[145]={name="O"} -62: atom[146]={name="N"} -62: atom[147]={name="H"} -62: atom[148]={name="CA"} -62: atom[149]={name="HA"} -62: atom[150]={name="CB"} -62: atom[151]={name="HB1"} -62: atom[152]={name="HB2"} -62: atom[153]={name="HB3"} -62: atom[154]={name="C"} -62: atom[155]={name="O"} -62: type (156): -62: type[0]={name="opls_287",nameB="opls_287"} -62: type[1]={name="opls_290",nameB="opls_290"} -62: type[2]={name="opls_290",nameB="opls_290"} -62: type[3]={name="opls_290",nameB="opls_290"} -62: type[4]={name="opls_293B",nameB="opls_293B"} -62: type[5]={name="opls_140",nameB="opls_140"} -62: type[6]={name="opls_136",nameB="opls_136"} -62: type[7]={name="opls_140",nameB="opls_140"} -62: type[8]={name="opls_140",nameB="opls_140"} -62: type[9]={name="opls_136",nameB="opls_136"} -62: type[10]={name="opls_140",nameB="opls_140"} -62: type[11]={name="opls_140",nameB="opls_140"} -62: type[12]={name="opls_136",nameB="opls_136"} -62: type[13]={name="opls_140",nameB="opls_140"} -62: type[14]={name="opls_140",nameB="opls_140"} -62: type[15]={name="opls_292",nameB="opls_292"} -62: type[16]={name="opls_140",nameB="opls_140"} -62: type[17]={name="opls_140",nameB="opls_140"} -62: type[18]={name="opls_287",nameB="opls_287"} -62: type[19]={name="opls_290",nameB="opls_290"} -62: type[20]={name="opls_290",nameB="opls_290"} -62: type[21]={name="opls_290",nameB="opls_290"} -62: type[22]={name="opls_235",nameB="opls_235"} -62: type[23]={name="opls_236",nameB="opls_236"} -62: type[24]={name="opls_238",nameB="opls_238"} -62: type[25]={name="opls_241",nameB="opls_241"} -62: type[26]={name="opls_224B",nameB="opls_224B"} -62: type[27]={name="opls_140",nameB="opls_140"} -62: type[28]={name="opls_137",nameB="opls_137"} -62: type[29]={name="opls_140",nameB="opls_140"} -62: type[30]={name="opls_135",nameB="opls_135"} -62: type[31]={name="opls_140",nameB="opls_140"} -62: type[32]={name="opls_140",nameB="opls_140"} -62: type[33]={name="opls_140",nameB="opls_140"} -62: type[34]={name="opls_135",nameB="opls_135"} -62: type[35]={name="opls_140",nameB="opls_140"} -62: type[36]={name="opls_140",nameB="opls_140"} -62: type[37]={name="opls_140",nameB="opls_140"} -62: type[38]={name="opls_235",nameB="opls_235"} -62: type[39]={name="opls_236",nameB="opls_236"} -62: type[40]={name="opls_238",nameB="opls_238"} -62: type[41]={name="opls_241",nameB="opls_241"} -62: type[42]={name="opls_224B",nameB="opls_224B"} -62: type[43]={name="opls_140",nameB="opls_140"} -62: type[44]={name="opls_149",nameB="opls_149"} -62: type[45]={name="opls_140",nameB="opls_140"} -62: type[46]={name="opls_140",nameB="opls_140"} -62: type[47]={name="opls_145",nameB="opls_145"} -62: type[48]={name="opls_145",nameB="opls_145"} -62: type[49]={name="opls_146",nameB="opls_146"} -62: type[50]={name="opls_145",nameB="opls_145"} -62: type[51]={name="opls_146",nameB="opls_146"} -62: type[52]={name="opls_145",nameB="opls_145"} -62: type[53]={name="opls_146",nameB="opls_146"} -62: type[54]={name="opls_145",nameB="opls_145"} -62: type[55]={name="opls_146",nameB="opls_146"} -62: type[56]={name="opls_145",nameB="opls_145"} -62: type[57]={name="opls_146",nameB="opls_146"} -62: type[58]={name="opls_235",nameB="opls_235"} -62: type[59]={name="opls_236",nameB="opls_236"} -62: type[60]={name="opls_238",nameB="opls_238"} -62: type[61]={name="opls_241",nameB="opls_241"} -62: type[62]={name="opls_223B",nameB="opls_223B"} -62: type[63]={name="opls_140",nameB="opls_140"} -62: type[64]={name="opls_140",nameB="opls_140"} -62: type[65]={name="opls_235",nameB="opls_235"} -62: type[66]={name="opls_236",nameB="opls_236"} -62: type[67]={name="opls_238",nameB="opls_238"} -62: type[68]={name="opls_241",nameB="opls_241"} -62: type[69]={name="opls_224B",nameB="opls_224B"} -62: type[70]={name="opls_140",nameB="opls_140"} -62: type[71]={name="opls_136",nameB="opls_136"} -62: type[72]={name="opls_140",nameB="opls_140"} -62: type[73]={name="opls_140",nameB="opls_140"} -62: type[74]={name="opls_308",nameB="opls_308"} -62: type[75]={name="opls_140",nameB="opls_140"} -62: type[76]={name="opls_140",nameB="opls_140"} -62: type[77]={name="opls_307",nameB="opls_307"} -62: type[78]={name="opls_140",nameB="opls_140"} -62: type[79]={name="opls_140",nameB="opls_140"} -62: type[80]={name="opls_303",nameB="opls_303"} -62: type[81]={name="opls_304",nameB="opls_304"} -62: type[82]={name="opls_302",nameB="opls_302"} -62: type[83]={name="opls_300",nameB="opls_300"} -62: type[84]={name="opls_301",nameB="opls_301"} -62: type[85]={name="opls_301",nameB="opls_301"} -62: type[86]={name="opls_300",nameB="opls_300"} -62: type[87]={name="opls_301",nameB="opls_301"} -62: type[88]={name="opls_301",nameB="opls_301"} -62: type[89]={name="opls_235",nameB="opls_235"} -62: type[90]={name="opls_236",nameB="opls_236"} -62: type[91]={name="opls_238",nameB="opls_238"} -62: type[92]={name="opls_241",nameB="opls_241"} -62: type[93]={name="opls_224B",nameB="opls_224B"} -62: type[94]={name="opls_140",nameB="opls_140"} -62: type[95]={name="opls_206",nameB="opls_206"} -62: type[96]={name="opls_140",nameB="opls_140"} -62: type[97]={name="opls_140",nameB="opls_140"} -62: type[98]={name="opls_200",nameB="opls_200"} -62: type[99]={name="opls_204",nameB="opls_204"} -62: type[100]={name="opls_235",nameB="opls_235"} -62: type[101]={name="opls_236",nameB="opls_236"} -62: type[102]={name="opls_238",nameB="opls_238"} -62: type[103]={name="opls_241",nameB="opls_241"} -62: type[104]={name="opls_224B",nameB="opls_224B"} -62: type[105]={name="opls_140",nameB="opls_140"} -62: type[106]={name="opls_136",nameB="opls_136"} -62: type[107]={name="opls_140",nameB="opls_140"} -62: type[108]={name="opls_140",nameB="opls_140"} -62: type[109]={name="opls_274",nameB="opls_274"} -62: type[110]={name="opls_140",nameB="opls_140"} -62: type[111]={name="opls_140",nameB="opls_140"} -62: type[112]={name="opls_271",nameB="opls_271"} -62: type[113]={name="opls_272",nameB="opls_272"} -62: type[114]={name="opls_272",nameB="opls_272"} -62: type[115]={name="opls_235",nameB="opls_235"} -62: type[116]={name="opls_236",nameB="opls_236"} -62: type[117]={name="opls_238",nameB="opls_238"} -62: type[118]={name="opls_241",nameB="opls_241"} -62: type[119]={name="opls_224B",nameB="opls_224B"} -62: type[120]={name="opls_140",nameB="opls_140"} -62: type[121]={name="opls_136",nameB="opls_136"} -62: type[122]={name="opls_140",nameB="opls_140"} -62: type[123]={name="opls_140",nameB="opls_140"} -62: type[124]={name="opls_137",nameB="opls_137"} -62: type[125]={name="opls_140",nameB="opls_140"} -62: type[126]={name="opls_135",nameB="opls_135"} -62: type[127]={name="opls_140",nameB="opls_140"} -62: type[128]={name="opls_140",nameB="opls_140"} -62: type[129]={name="opls_140",nameB="opls_140"} -62: type[130]={name="opls_135",nameB="opls_135"} -62: type[131]={name="opls_140",nameB="opls_140"} -62: type[132]={name="opls_140",nameB="opls_140"} -62: type[133]={name="opls_140",nameB="opls_140"} -62: type[134]={name="opls_235",nameB="opls_235"} -62: type[135]={name="opls_236",nameB="opls_236"} -62: type[136]={name="opls_238",nameB="opls_238"} -62: type[137]={name="opls_241",nameB="opls_241"} -62: type[138]={name="opls_224B",nameB="opls_224B"} -62: type[139]={name="opls_140",nameB="opls_140"} -62: type[140]={name="opls_135",nameB="opls_135"} -62: type[141]={name="opls_140",nameB="opls_140"} -62: type[142]={name="opls_140",nameB="opls_140"} -62: type[143]={name="opls_140",nameB="opls_140"} -62: type[144]={name="opls_235",nameB="opls_235"} -62: type[145]={name="opls_236",nameB="opls_236"} -62: type[146]={name="opls_238",nameB="opls_238"} -62: type[147]={name="opls_241",nameB="opls_241"} -62: type[148]={name="opls_224B",nameB="opls_224B"} -62: type[149]={name="opls_140",nameB="opls_140"} -62: type[150]={name="opls_135",nameB="opls_135"} -62: type[151]={name="opls_140",nameB="opls_140"} -62: type[152]={name="opls_140",nameB="opls_140"} -62: type[153]={name="opls_140",nameB="opls_140"} -62: type[154]={name="opls_235",nameB="opls_235"} -62: type[155]={name="opls_236",nameB="opls_236"} -62: residue (10): -62: residue[0]={name="LYS", nr=1, ic=' '} -62: residue[1]={name="VAL", nr=2, ic=' '} -62: residue[2]={name="PHE", nr=3, ic=' '} -62: residue[3]={name="GLY", nr=4, ic=' '} -62: residue[4]={name="ARG", nr=5, ic=' '} -62: residue[5]={name="CYS", nr=6, ic=' '} -62: residue[6]={name="GLU", nr=7, ic=' '} -62: residue[7]={name="LEU", nr=8, ic=' '} -62: residue[8]={name="ALA", nr=9, ic=' '} -62: residue[9]={name="ALA", nr=10, ic=' '} -62: excls: -62: numLists=156 -62: numElements=1828 -62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, -62: 23, 24, 25, 26} -62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, -62: 14, 15, 22, 23, 24} -62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -62: 16, 17, 18, 22} -62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, -62: 17, 18, 19, 20, 21} -62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, -62: 20, 21} -62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, -62: 26, 27, 28, 38} -62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} -62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, -62: 30, 34, 38, 39, 40} -62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} -62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, -62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} -62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -62: 40} -62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, -62: 34, 35, 36, 37, 38, 39, 40} -62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -62: 36, 37, 38} -62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -62: 40, 41, 42, 43, 44, 58} -62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} -62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, -62: 45, 46, 47, 58, 59, 60} -62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} -62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, -62: 48, 50, 58, 59, 60, 61, 62} -62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -62: 60} -62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, -62: 50, 51, 52, 54, 58, 59, 60} -62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, -62: 52, 53, 54, 55, 56, 58} -62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, -62: 54, 56, 57} -62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} -62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, -62: 55, 56, 57} -62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} -62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} -62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} -62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} -62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} -62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} -62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} -62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -62: 60, 61, 62, 63, 64, 65} -62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} -62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, -62: 65, 66, 67} -62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} -62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, -62: 68, 69} -62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, -62: 70, 71, 89} -62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} -62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, -62: 72, 73, 74, 89, 90, 91} -62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} -62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, -62: 75, 76, 77, 89, 90, 91, 92, 93} -62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -62: 91} -62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, -62: 77, 78, 79, 80, 89, 90, 91} -62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, -62: 79, 80, 81, 82, 89} -62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, -62: 81, 82, 83, 86} -62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, -62: 84, 85, 86, 87, 88} -62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} -62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, -62: 87, 88} -62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -62: excls[84][num=6]={80, 82, 83, 84, 85, 86} -62: excls[85][num=6]={80, 82, 83, 84, 85, 86} -62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -62: excls[87][num=6]={80, 82, 83, 86, 87, 88} -62: excls[88][num=6]={80, 82, 83, 86, 87, 88} -62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -62: 91, 92, 93, 94, 95, 100} -62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} -62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, -62: 96, 97, 98, 100, 101, 102} -62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} -62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, -62: 99, 100, 101, 102, 103, 104} -62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -62: 102} -62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, -62: 101, 102} -62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -62: excls[99][num=6]={93, 95, 96, 97, 98, 99} -62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -62: 102, 103, 104, 105, 106, 115} -62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} -62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, -62: 106, 107, 108, 109, 115, 116, 117} -62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} -62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, -62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} -62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 115, 116, 117} -62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 110, 111, 112, 113, 114, 115, 116, 117} -62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 115} -62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 115} -62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, -62: 112, 113, 114, 115} -62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -62: 114} -62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} -62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} -62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -62: 115, 116, 117, 118, 119, 120, 121, 134} -62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} -62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, -62: 120, 121, 122, 123, 124, 134, 135, 136} -62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} -62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, -62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} -62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 134, 135, 136} -62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} -62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 130, 134} -62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 130, 134} -62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, -62: 127, 128, 129, 130, 131, 132, 133, 134} -62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -62: 129, 130, 131, 132, 133} -62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, -62: 134, 135, 136, 137, 138, 139, 140, 144} -62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} -62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, -62: 139, 140, 141, 142, 143, 144, 145, 146} -62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} -62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, -62: 142, 143, 144, 145, 146, 147, 148} -62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146} -62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146} -62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, -62: 144, 145, 146, 147, 148, 149, 150, 154} -62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} -62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, -62: 149, 150, 151, 152, 153, 154, 155} -62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} -62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, -62: 152, 153, 154, 155} -62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -62: 154, 155} -62: excls[155][num=6]={146, 148, 149, 150, 154, 155} -62: Bond: -62: nr: 468 -62: iatoms: -62: 0 type=100 (BONDS) 0 1 -62: 1 type=100 (BONDS) 0 2 -62: 2 type=100 (BONDS) 0 3 -62: 3 type=101 (BONDS) 0 4 -62: 4 type=102 (BONDS) 4 5 -62: 5 type=103 (BONDS) 4 6 -62: 6 type=104 (BONDS) 4 22 -62: 7 type=102 (BONDS) 6 7 -62: 8 type=102 (BONDS) 6 8 -62: 9 type=103 (BONDS) 6 9 -62: 10 type=102 (BONDS) 9 10 -62: 11 type=102 (BONDS) 9 11 -62: 12 type=103 (BONDS) 9 12 -62: 13 type=102 (BONDS) 12 13 -62: 14 type=102 (BONDS) 12 14 -62: 15 type=103 (BONDS) 12 15 -62: 16 type=102 (BONDS) 15 16 -62: 17 type=102 (BONDS) 15 17 -62: 18 type=101 (BONDS) 15 18 -62: 19 type=100 (BONDS) 18 19 -62: 20 type=100 (BONDS) 18 20 -62: 21 type=100 (BONDS) 18 21 -62: 22 type=105 (BONDS) 22 23 -62: 23 type=106 (BONDS) 22 24 -62: 24 type=100 (BONDS) 24 25 -62: 25 type=107 (BONDS) 24 26 -62: 26 type=102 (BONDS) 26 27 -62: 27 type=103 (BONDS) 26 28 -62: 28 type=104 (BONDS) 26 38 -62: 29 type=102 (BONDS) 28 29 -62: 30 type=103 (BONDS) 28 30 -62: 31 type=103 (BONDS) 28 34 -62: 32 type=102 (BONDS) 30 31 -62: 33 type=102 (BONDS) 30 32 -62: 34 type=102 (BONDS) 30 33 -62: 35 type=102 (BONDS) 34 35 -62: 36 type=102 (BONDS) 34 36 -62: 37 type=102 (BONDS) 34 37 -62: 38 type=105 (BONDS) 38 39 -62: 39 type=106 (BONDS) 38 40 -62: 40 type=100 (BONDS) 40 41 -62: 41 type=107 (BONDS) 40 42 -62: 42 type=102 (BONDS) 42 43 -62: 43 type=103 (BONDS) 42 44 -62: 44 type=104 (BONDS) 42 58 -62: 45 type=102 (BONDS) 44 45 -62: 46 type=102 (BONDS) 44 46 -62: 47 type=108 (BONDS) 44 47 -62: 48 type=109 (BONDS) 47 48 -62: 49 type=109 (BONDS) 47 50 -62: 50 type=110 (BONDS) 48 49 -62: 51 type=109 (BONDS) 48 52 -62: 52 type=110 (BONDS) 50 51 -62: 53 type=109 (BONDS) 50 54 -62: 54 type=110 (BONDS) 52 53 -62: 55 type=109 (BONDS) 52 56 -62: 56 type=110 (BONDS) 54 55 -62: 57 type=109 (BONDS) 54 56 -62: 58 type=110 (BONDS) 56 57 -62: 59 type=105 (BONDS) 58 59 -62: 60 type=106 (BONDS) 58 60 -62: 61 type=100 (BONDS) 60 61 -62: 62 type=107 (BONDS) 60 62 -62: 63 type=102 (BONDS) 62 63 -62: 64 type=102 (BONDS) 62 64 -62: 65 type=104 (BONDS) 62 65 -62: 66 type=105 (BONDS) 65 66 -62: 67 type=106 (BONDS) 65 67 -62: 68 type=100 (BONDS) 67 68 -62: 69 type=107 (BONDS) 67 69 -62: 70 type=102 (BONDS) 69 70 -62: 71 type=103 (BONDS) 69 71 -62: 72 type=104 (BONDS) 69 89 -62: 73 type=102 (BONDS) 71 72 -62: 74 type=102 (BONDS) 71 73 -62: 75 type=103 (BONDS) 71 74 -62: 76 type=102 (BONDS) 74 75 -62: 77 type=102 (BONDS) 74 76 -62: 78 type=103 (BONDS) 74 77 -62: 79 type=102 (BONDS) 77 78 -62: 80 type=102 (BONDS) 77 79 -62: 81 type=111 (BONDS) 77 80 -62: 82 type=100 (BONDS) 80 81 -62: 83 type=112 (BONDS) 80 82 -62: 84 type=112 (BONDS) 82 83 -62: 85 type=112 (BONDS) 82 86 -62: 86 type=100 (BONDS) 83 84 -62: 87 type=100 (BONDS) 83 85 -62: 88 type=100 (BONDS) 86 87 -62: 89 type=100 (BONDS) 86 88 -62: 90 type=105 (BONDS) 89 90 -62: 91 type=106 (BONDS) 89 91 -62: 92 type=100 (BONDS) 91 92 -62: 93 type=107 (BONDS) 91 93 -62: 94 type=102 (BONDS) 93 94 -62: 95 type=103 (BONDS) 93 95 -62: 96 type=104 (BONDS) 93 100 -62: 97 type=102 (BONDS) 95 96 -62: 98 type=102 (BONDS) 95 97 -62: 99 type=113 (BONDS) 95 98 -62: 100 type=114 (BONDS) 98 99 -62: 101 type=105 (BONDS) 100 101 -62: 102 type=106 (BONDS) 100 102 -62: 103 type=100 (BONDS) 102 103 -62: 104 type=107 (BONDS) 102 104 -62: 105 type=102 (BONDS) 104 105 -62: 106 type=103 (BONDS) 104 106 -62: 107 type=104 (BONDS) 104 115 -62: 108 type=102 (BONDS) 106 107 -62: 109 type=102 (BONDS) 106 108 -62: 110 type=103 (BONDS) 106 109 -62: 111 type=102 (BONDS) 109 110 -62: 112 type=102 (BONDS) 109 111 -62: 113 type=104 (BONDS) 109 112 -62: 114 type=115 (BONDS) 112 113 -62: 115 type=115 (BONDS) 112 114 -62: 116 type=105 (BONDS) 115 116 -62: 117 type=106 (BONDS) 115 117 -62: 118 type=100 (BONDS) 117 118 -62: 119 type=107 (BONDS) 117 119 -62: 120 type=102 (BONDS) 119 120 -62: 121 type=103 (BONDS) 119 121 -62: 122 type=104 (BONDS) 119 134 -62: 123 type=102 (BONDS) 121 122 -62: 124 type=102 (BONDS) 121 123 -62: 125 type=103 (BONDS) 121 124 -62: 126 type=102 (BONDS) 124 125 -62: 127 type=103 (BONDS) 124 126 -62: 128 type=103 (BONDS) 124 130 -62: 129 type=102 (BONDS) 126 127 -62: 130 type=102 (BONDS) 126 128 -62: 131 type=102 (BONDS) 126 129 -62: 132 type=102 (BONDS) 130 131 -62: 133 type=102 (BONDS) 130 132 -62: 134 type=102 (BONDS) 130 133 -62: 135 type=105 (BONDS) 134 135 -62: 136 type=106 (BONDS) 134 136 -62: 137 type=100 (BONDS) 136 137 -62: 138 type=107 (BONDS) 136 138 -62: 139 type=102 (BONDS) 138 139 -62: 140 type=103 (BONDS) 138 140 -62: 141 type=104 (BONDS) 138 144 -62: 142 type=102 (BONDS) 140 141 -62: 143 type=102 (BONDS) 140 142 -62: 144 type=102 (BONDS) 140 143 -62: 145 type=105 (BONDS) 144 145 -62: 146 type=106 (BONDS) 144 146 -62: 147 type=100 (BONDS) 146 147 -62: 148 type=107 (BONDS) 146 148 -62: 149 type=102 (BONDS) 148 149 -62: 150 type=103 (BONDS) 148 150 -62: 151 type=104 (BONDS) 148 154 -62: 152 type=102 (BONDS) 150 151 -62: 153 type=102 (BONDS) 150 152 -62: 154 type=102 (BONDS) 150 153 -62: 155 type=105 (BONDS) 154 155 -62: G96Bond: -62: nr: 0 -62: Morse: -62: nr: 0 -62: Cubic Bonds: -62: nr: 0 -62: Connect Bonds: -62: nr: 0 -62: Harmonic Pot.: -62: nr: 0 -62: FENE Bonds: -62: nr: 0 -62: Tab. Bonds: -62: nr: 0 -62: Tab. Bonds NC: -62: nr: 0 -62: Restraint Pot.: -62: nr: 0 -62: Angle: -62: nr: 1124 -62: iatoms: -62: 0 type=116 (ANGLES) 1 0 2 -62: 1 type=116 (ANGLES) 1 0 3 -62: 2 type=116 (ANGLES) 1 0 4 -62: 3 type=116 (ANGLES) 2 0 3 -62: 4 type=116 (ANGLES) 2 0 4 -62: 5 type=116 (ANGLES) 3 0 4 -62: 6 type=116 (ANGLES) 0 4 5 -62: 7 type=117 (ANGLES) 0 4 6 -62: 8 type=117 (ANGLES) 0 4 22 -62: 9 type=118 (ANGLES) 5 4 6 -62: 10 type=116 (ANGLES) 5 4 22 -62: 11 type=119 (ANGLES) 6 4 22 -62: 12 type=118 (ANGLES) 4 6 7 -62: 13 type=118 (ANGLES) 4 6 8 -62: 14 type=120 (ANGLES) 4 6 9 -62: 15 type=121 (ANGLES) 7 6 8 -62: 16 type=118 (ANGLES) 7 6 9 -62: 17 type=118 (ANGLES) 8 6 9 -62: 18 type=118 (ANGLES) 6 9 10 -62: 19 type=118 (ANGLES) 6 9 11 -62: 20 type=120 (ANGLES) 6 9 12 -62: 21 type=121 (ANGLES) 10 9 11 -62: 22 type=118 (ANGLES) 10 9 12 -62: 23 type=118 (ANGLES) 11 9 12 -62: 24 type=118 (ANGLES) 9 12 13 -62: 25 type=118 (ANGLES) 9 12 14 -62: 26 type=120 (ANGLES) 9 12 15 -62: 27 type=121 (ANGLES) 13 12 14 -62: 28 type=118 (ANGLES) 13 12 15 -62: 29 type=118 (ANGLES) 14 12 15 -62: 30 type=118 (ANGLES) 12 15 16 -62: 31 type=118 (ANGLES) 12 15 17 -62: 32 type=117 (ANGLES) 12 15 18 -62: 33 type=121 (ANGLES) 16 15 17 -62: 34 type=116 (ANGLES) 16 15 18 -62: 35 type=116 (ANGLES) 17 15 18 -62: 36 type=116 (ANGLES) 15 18 19 -62: 37 type=116 (ANGLES) 15 18 20 -62: 38 type=116 (ANGLES) 15 18 21 -62: 39 type=116 (ANGLES) 19 18 20 -62: 40 type=116 (ANGLES) 19 18 21 -62: 41 type=116 (ANGLES) 20 18 21 -62: 42 type=122 (ANGLES) 4 22 23 -62: 43 type=123 (ANGLES) 4 22 24 -62: 44 type=124 (ANGLES) 23 22 24 -62: 45 type=125 (ANGLES) 22 24 25 -62: 46 type=126 (ANGLES) 22 24 26 -62: 47 type=127 (ANGLES) 25 24 26 -62: 48 type=116 (ANGLES) 24 26 27 -62: 49 type=128 (ANGLES) 24 26 28 -62: 50 type=129 (ANGLES) 24 26 38 -62: 51 type=118 (ANGLES) 27 26 28 -62: 52 type=116 (ANGLES) 27 26 38 -62: 53 type=119 (ANGLES) 28 26 38 -62: 54 type=118 (ANGLES) 26 28 29 -62: 55 type=120 (ANGLES) 26 28 30 -62: 56 type=120 (ANGLES) 26 28 34 -62: 57 type=118 (ANGLES) 29 28 30 -62: 58 type=118 (ANGLES) 29 28 34 -62: 59 type=120 (ANGLES) 30 28 34 -62: 60 type=118 (ANGLES) 28 30 31 -62: 61 type=118 (ANGLES) 28 30 32 -62: 62 type=118 (ANGLES) 28 30 33 -62: 63 type=121 (ANGLES) 31 30 32 -62: 64 type=121 (ANGLES) 31 30 33 -62: 65 type=121 (ANGLES) 32 30 33 -62: 66 type=118 (ANGLES) 28 34 35 -62: 67 type=118 (ANGLES) 28 34 36 -62: 68 type=118 (ANGLES) 28 34 37 -62: 69 type=121 (ANGLES) 35 34 36 -62: 70 type=121 (ANGLES) 35 34 37 -62: 71 type=121 (ANGLES) 36 34 37 -62: 72 type=122 (ANGLES) 26 38 39 -62: 73 type=123 (ANGLES) 26 38 40 -62: 74 type=124 (ANGLES) 39 38 40 -62: 75 type=125 (ANGLES) 38 40 41 -62: 76 type=126 (ANGLES) 38 40 42 -62: 77 type=127 (ANGLES) 41 40 42 -62: 78 type=116 (ANGLES) 40 42 43 -62: 79 type=128 (ANGLES) 40 42 44 -62: 80 type=129 (ANGLES) 40 42 58 -62: 81 type=118 (ANGLES) 43 42 44 -62: 82 type=116 (ANGLES) 43 42 58 -62: 83 type=119 (ANGLES) 44 42 58 -62: 84 type=118 (ANGLES) 42 44 45 -62: 85 type=118 (ANGLES) 42 44 46 -62: 86 type=130 (ANGLES) 42 44 47 -62: 87 type=121 (ANGLES) 45 44 46 -62: 88 type=116 (ANGLES) 45 44 47 -62: 89 type=116 (ANGLES) 46 44 47 -62: 90 type=131 (ANGLES) 44 47 48 -62: 91 type=131 (ANGLES) 44 47 50 -62: 92 type=132 (ANGLES) 48 47 50 -62: 93 type=133 (ANGLES) 47 48 49 -62: 94 type=132 (ANGLES) 47 48 52 -62: 95 type=133 (ANGLES) 49 48 52 -62: 96 type=133 (ANGLES) 47 50 51 -62: 97 type=132 (ANGLES) 47 50 54 -62: 98 type=133 (ANGLES) 51 50 54 -62: 99 type=133 (ANGLES) 48 52 53 -62: 100 type=132 (ANGLES) 48 52 56 -62: 101 type=133 (ANGLES) 53 52 56 -62: 102 type=133 (ANGLES) 50 54 55 -62: 103 type=132 (ANGLES) 50 54 56 -62: 104 type=133 (ANGLES) 55 54 56 -62: 105 type=132 (ANGLES) 52 56 54 -62: 106 type=133 (ANGLES) 52 56 57 -62: 107 type=133 (ANGLES) 54 56 57 -62: 108 type=122 (ANGLES) 42 58 59 -62: 109 type=123 (ANGLES) 42 58 60 -62: 110 type=124 (ANGLES) 59 58 60 -62: 111 type=125 (ANGLES) 58 60 61 -62: 112 type=126 (ANGLES) 58 60 62 -62: 113 type=127 (ANGLES) 61 60 62 -62: 114 type=116 (ANGLES) 60 62 63 -62: 115 type=116 (ANGLES) 60 62 64 -62: 116 type=129 (ANGLES) 60 62 65 -62: 117 type=121 (ANGLES) 63 62 64 -62: 118 type=116 (ANGLES) 63 62 65 -62: 119 type=116 (ANGLES) 64 62 65 -62: 120 type=122 (ANGLES) 62 65 66 -62: 121 type=123 (ANGLES) 62 65 67 -62: 122 type=124 (ANGLES) 66 65 67 -62: 123 type=125 (ANGLES) 65 67 68 -62: 124 type=126 (ANGLES) 65 67 69 -62: 125 type=127 (ANGLES) 68 67 69 -62: 126 type=116 (ANGLES) 67 69 70 -62: 127 type=128 (ANGLES) 67 69 71 -62: 128 type=129 (ANGLES) 67 69 89 -62: 129 type=118 (ANGLES) 70 69 71 -62: 130 type=116 (ANGLES) 70 69 89 -62: 131 type=119 (ANGLES) 71 69 89 -62: 132 type=118 (ANGLES) 69 71 72 -62: 133 type=118 (ANGLES) 69 71 73 -62: 134 type=120 (ANGLES) 69 71 74 -62: 135 type=121 (ANGLES) 72 71 73 -62: 136 type=118 (ANGLES) 72 71 74 -62: 137 type=118 (ANGLES) 73 71 74 -62: 138 type=118 (ANGLES) 71 74 75 -62: 139 type=118 (ANGLES) 71 74 76 -62: 140 type=120 (ANGLES) 71 74 77 -62: 141 type=121 (ANGLES) 75 74 76 -62: 142 type=118 (ANGLES) 75 74 77 -62: 143 type=118 (ANGLES) 76 74 77 -62: 144 type=118 (ANGLES) 74 77 78 -62: 145 type=118 (ANGLES) 74 77 79 -62: 146 type=117 (ANGLES) 74 77 80 -62: 147 type=121 (ANGLES) 78 77 79 -62: 148 type=116 (ANGLES) 78 77 80 -62: 149 type=116 (ANGLES) 79 77 80 -62: 150 type=134 (ANGLES) 77 80 81 -62: 151 type=135 (ANGLES) 77 80 82 -62: 152 type=133 (ANGLES) 81 80 82 -62: 153 type=131 (ANGLES) 80 82 83 -62: 154 type=131 (ANGLES) 80 82 86 -62: 155 type=131 (ANGLES) 83 82 86 -62: 156 type=133 (ANGLES) 82 83 84 -62: 157 type=133 (ANGLES) 82 83 85 -62: 158 type=133 (ANGLES) 84 83 85 -62: 159 type=133 (ANGLES) 82 86 87 -62: 160 type=133 (ANGLES) 82 86 88 -62: 161 type=133 (ANGLES) 87 86 88 -62: 162 type=122 (ANGLES) 69 89 90 -62: 163 type=123 (ANGLES) 69 89 91 -62: 164 type=124 (ANGLES) 90 89 91 -62: 165 type=125 (ANGLES) 89 91 92 -62: 166 type=126 (ANGLES) 89 91 93 -62: 167 type=127 (ANGLES) 92 91 93 -62: 168 type=116 (ANGLES) 91 93 94 -62: 169 type=128 (ANGLES) 91 93 95 -62: 170 type=129 (ANGLES) 91 93 100 -62: 171 type=118 (ANGLES) 94 93 95 -62: 172 type=116 (ANGLES) 94 93 100 -62: 173 type=119 (ANGLES) 95 93 100 -62: 174 type=118 (ANGLES) 93 95 96 -62: 175 type=118 (ANGLES) 93 95 97 -62: 176 type=136 (ANGLES) 93 95 98 -62: 177 type=121 (ANGLES) 96 95 97 -62: 178 type=116 (ANGLES) 96 95 98 -62: 179 type=116 (ANGLES) 97 95 98 -62: 180 type=137 (ANGLES) 95 98 99 -62: 181 type=122 (ANGLES) 93 100 101 -62: 182 type=123 (ANGLES) 93 100 102 -62: 183 type=124 (ANGLES) 101 100 102 -62: 184 type=125 (ANGLES) 100 102 103 -62: 185 type=126 (ANGLES) 100 102 104 -62: 186 type=127 (ANGLES) 103 102 104 -62: 187 type=116 (ANGLES) 102 104 105 -62: 188 type=128 (ANGLES) 102 104 106 -62: 189 type=129 (ANGLES) 102 104 115 -62: 190 type=118 (ANGLES) 105 104 106 -62: 191 type=116 (ANGLES) 105 104 115 -62: 192 type=119 (ANGLES) 106 104 115 -62: 193 type=118 (ANGLES) 104 106 107 -62: 194 type=118 (ANGLES) 104 106 108 -62: 195 type=120 (ANGLES) 104 106 109 -62: 196 type=121 (ANGLES) 107 106 108 -62: 197 type=118 (ANGLES) 107 106 109 -62: 198 type=118 (ANGLES) 108 106 109 -62: 199 type=118 (ANGLES) 106 109 110 -62: 200 type=118 (ANGLES) 106 109 111 -62: 201 type=119 (ANGLES) 106 109 112 -62: 202 type=121 (ANGLES) 110 109 111 -62: 203 type=116 (ANGLES) 110 109 112 -62: 204 type=116 (ANGLES) 111 109 112 -62: 205 type=138 (ANGLES) 109 112 113 -62: 206 type=138 (ANGLES) 109 112 114 -62: 207 type=139 (ANGLES) 113 112 114 -62: 208 type=122 (ANGLES) 104 115 116 -62: 209 type=123 (ANGLES) 104 115 117 -62: 210 type=124 (ANGLES) 116 115 117 -62: 211 type=125 (ANGLES) 115 117 118 -62: 212 type=126 (ANGLES) 115 117 119 -62: 213 type=127 (ANGLES) 118 117 119 -62: 214 type=116 (ANGLES) 117 119 120 -62: 215 type=128 (ANGLES) 117 119 121 -62: 216 type=129 (ANGLES) 117 119 134 -62: 217 type=118 (ANGLES) 120 119 121 -62: 218 type=116 (ANGLES) 120 119 134 -62: 219 type=119 (ANGLES) 121 119 134 -62: 220 type=118 (ANGLES) 119 121 122 -62: 221 type=118 (ANGLES) 119 121 123 -62: 222 type=120 (ANGLES) 119 121 124 -62: 223 type=121 (ANGLES) 122 121 123 -62: 224 type=118 (ANGLES) 122 121 124 -62: 225 type=118 (ANGLES) 123 121 124 -62: 226 type=118 (ANGLES) 121 124 125 -62: 227 type=120 (ANGLES) 121 124 126 -62: 228 type=120 (ANGLES) 121 124 130 -62: 229 type=118 (ANGLES) 125 124 126 -62: 230 type=118 (ANGLES) 125 124 130 -62: 231 type=120 (ANGLES) 126 124 130 -62: 232 type=118 (ANGLES) 124 126 127 -62: 233 type=118 (ANGLES) 124 126 128 -62: 234 type=118 (ANGLES) 124 126 129 -62: 235 type=121 (ANGLES) 127 126 128 -62: 236 type=121 (ANGLES) 127 126 129 -62: 237 type=121 (ANGLES) 128 126 129 -62: 238 type=118 (ANGLES) 124 130 131 -62: 239 type=118 (ANGLES) 124 130 132 -62: 240 type=118 (ANGLES) 124 130 133 -62: 241 type=121 (ANGLES) 131 130 132 -62: 242 type=121 (ANGLES) 131 130 133 -62: 243 type=121 (ANGLES) 132 130 133 -62: 244 type=122 (ANGLES) 119 134 135 -62: 245 type=123 (ANGLES) 119 134 136 -62: 246 type=124 (ANGLES) 135 134 136 -62: 247 type=125 (ANGLES) 134 136 137 -62: 248 type=126 (ANGLES) 134 136 138 -62: 249 type=127 (ANGLES) 137 136 138 -62: 250 type=116 (ANGLES) 136 138 139 -62: 251 type=128 (ANGLES) 136 138 140 -62: 252 type=129 (ANGLES) 136 138 144 -62: 253 type=118 (ANGLES) 139 138 140 -62: 254 type=116 (ANGLES) 139 138 144 -62: 255 type=119 (ANGLES) 140 138 144 -62: 256 type=118 (ANGLES) 138 140 141 -62: 257 type=118 (ANGLES) 138 140 142 -62: 258 type=118 (ANGLES) 138 140 143 -62: 259 type=121 (ANGLES) 141 140 142 -62: 260 type=121 (ANGLES) 141 140 143 -62: 261 type=121 (ANGLES) 142 140 143 -62: 262 type=122 (ANGLES) 138 144 145 -62: 263 type=123 (ANGLES) 138 144 146 -62: 264 type=124 (ANGLES) 145 144 146 -62: 265 type=125 (ANGLES) 144 146 147 -62: 266 type=126 (ANGLES) 144 146 148 -62: 267 type=127 (ANGLES) 147 146 148 -62: 268 type=116 (ANGLES) 146 148 149 -62: 269 type=128 (ANGLES) 146 148 150 -62: 270 type=129 (ANGLES) 146 148 154 -62: 271 type=118 (ANGLES) 149 148 150 -62: 272 type=116 (ANGLES) 149 148 154 -62: 273 type=119 (ANGLES) 150 148 154 -62: 274 type=118 (ANGLES) 148 150 151 -62: 275 type=118 (ANGLES) 148 150 152 -62: 276 type=118 (ANGLES) 148 150 153 -62: 277 type=121 (ANGLES) 151 150 152 -62: 278 type=121 (ANGLES) 151 150 153 -62: 279 type=121 (ANGLES) 152 150 153 -62: 280 type=122 (ANGLES) 148 154 155 -62: G96Angle: -62: nr: 0 -62: Restr. Angles: -62: nr: 0 -62: Lin. Angle: -62: nr: 0 -62: Bond-Cross: -62: nr: 0 -62: BA-Cross: -62: nr: 0 -62: U-B: -62: nr: 0 -62: Quartic Angles: -62: nr: 0 -62: Tab. Angles: -62: nr: 0 -62: Proper Dih.: -62: nr: 145 -62: iatoms: -62: 0 type=140 (PDIHS) 4 24 22 23 -62: 1 type=141 (PDIHS) 22 26 24 25 -62: 2 type=140 (PDIHS) 26 40 38 39 -62: 3 type=141 (PDIHS) 38 42 40 41 -62: 4 type=140 (PDIHS) 42 60 58 59 -62: 5 type=142 (PDIHS) 44 47 50 48 -62: 6 type=142 (PDIHS) 47 52 48 49 -62: 7 type=142 (PDIHS) 47 54 50 51 -62: 8 type=142 (PDIHS) 48 56 52 53 -62: 9 type=142 (PDIHS) 50 56 54 55 -62: 10 type=142 (PDIHS) 52 54 56 57 -62: 11 type=141 (PDIHS) 58 62 60 61 -62: 12 type=140 (PDIHS) 62 67 65 66 -62: 13 type=141 (PDIHS) 65 69 67 68 -62: 14 type=140 (PDIHS) 69 91 89 90 -62: 15 type=141 (PDIHS) 77 82 80 81 -62: 16 type=140 (PDIHS) 80 83 82 86 -62: 17 type=141 (PDIHS) 82 84 83 85 -62: 18 type=141 (PDIHS) 82 87 86 88 -62: 19 type=141 (PDIHS) 89 93 91 92 -62: 20 type=140 (PDIHS) 93 102 100 101 -62: 21 type=141 (PDIHS) 100 104 102 103 -62: 22 type=140 (PDIHS) 104 117 115 116 -62: 23 type=140 (PDIHS) 109 113 112 114 -62: 24 type=141 (PDIHS) 115 119 117 118 -62: 25 type=140 (PDIHS) 119 136 134 135 -62: 26 type=141 (PDIHS) 134 138 136 137 -62: 27 type=140 (PDIHS) 138 146 144 145 -62: 28 type=141 (PDIHS) 144 148 146 147 -62: Ryckaert-Bell.: -62: nr: 1565 -62: iatoms: -62: 0 type=143 (RBDIHS) 1 0 4 5 -62: 1 type=144 (RBDIHS) 1 0 4 6 -62: 2 type=144 (RBDIHS) 1 0 4 22 -62: 3 type=143 (RBDIHS) 2 0 4 5 -62: 4 type=144 (RBDIHS) 2 0 4 6 -62: 5 type=144 (RBDIHS) 2 0 4 22 -62: 6 type=143 (RBDIHS) 3 0 4 5 -62: 7 type=144 (RBDIHS) 3 0 4 6 -62: 8 type=144 (RBDIHS) 3 0 4 22 -62: 9 type=145 (RBDIHS) 0 4 6 9 -62: 10 type=146 (RBDIHS) 22 4 6 9 -62: 11 type=147 (RBDIHS) 0 4 6 7 -62: 12 type=147 (RBDIHS) 0 4 6 8 -62: 13 type=148 (RBDIHS) 5 4 6 7 -62: 14 type=148 (RBDIHS) 5 4 6 8 -62: 15 type=148 (RBDIHS) 5 4 6 9 -62: 16 type=149 (RBDIHS) 22 4 6 7 -62: 17 type=149 (RBDIHS) 22 4 6 8 -62: 18 type=150 (RBDIHS) 0 4 22 24 -62: 19 type=151 (RBDIHS) 6 4 22 24 -62: 20 type=148 (RBDIHS) 4 6 9 10 -62: 21 type=148 (RBDIHS) 4 6 9 11 -62: 22 type=152 (RBDIHS) 4 6 9 12 -62: 23 type=148 (RBDIHS) 7 6 9 10 -62: 24 type=148 (RBDIHS) 7 6 9 11 -62: 25 type=148 (RBDIHS) 7 6 9 12 -62: 26 type=148 (RBDIHS) 8 6 9 10 -62: 27 type=148 (RBDIHS) 8 6 9 11 -62: 28 type=148 (RBDIHS) 8 6 9 12 -62: 29 type=148 (RBDIHS) 6 9 12 13 -62: 30 type=148 (RBDIHS) 6 9 12 14 -62: 31 type=152 (RBDIHS) 6 9 12 15 -62: 32 type=148 (RBDIHS) 10 9 12 13 -62: 33 type=148 (RBDIHS) 10 9 12 14 -62: 34 type=148 (RBDIHS) 10 9 12 15 -62: 35 type=148 (RBDIHS) 11 9 12 13 -62: 36 type=148 (RBDIHS) 11 9 12 14 -62: 37 type=148 (RBDIHS) 11 9 12 15 -62: 38 type=148 (RBDIHS) 9 12 15 16 -62: 39 type=148 (RBDIHS) 9 12 15 17 -62: 40 type=153 (RBDIHS) 9 12 15 18 -62: 41 type=148 (RBDIHS) 13 12 15 16 -62: 42 type=148 (RBDIHS) 13 12 15 17 -62: 43 type=154 (RBDIHS) 13 12 15 18 -62: 44 type=148 (RBDIHS) 14 12 15 16 -62: 45 type=148 (RBDIHS) 14 12 15 17 -62: 46 type=154 (RBDIHS) 14 12 15 18 -62: 47 type=144 (RBDIHS) 12 15 18 19 -62: 48 type=144 (RBDIHS) 12 15 18 20 -62: 49 type=144 (RBDIHS) 12 15 18 21 -62: 50 type=143 (RBDIHS) 16 15 18 19 -62: 51 type=143 (RBDIHS) 16 15 18 20 -62: 52 type=143 (RBDIHS) 16 15 18 21 -62: 53 type=143 (RBDIHS) 17 15 18 19 -62: 54 type=143 (RBDIHS) 17 15 18 20 -62: 55 type=143 (RBDIHS) 17 15 18 21 -62: 56 type=155 (RBDIHS) 4 22 24 25 -62: 57 type=156 (RBDIHS) 4 22 24 26 -62: 58 type=155 (RBDIHS) 23 22 24 25 -62: 59 type=157 (RBDIHS) 23 22 24 26 -62: 60 type=158 (RBDIHS) 22 24 26 28 -62: 61 type=159 (RBDIHS) 22 24 26 38 -62: 62 type=160 (RBDIHS) 24 26 28 30 -62: 63 type=160 (RBDIHS) 24 26 28 34 -62: 64 type=161 (RBDIHS) 38 26 28 30 -62: 65 type=161 (RBDIHS) 38 26 28 34 -62: 66 type=147 (RBDIHS) 24 26 28 29 -62: 67 type=148 (RBDIHS) 27 26 28 29 -62: 68 type=148 (RBDIHS) 27 26 28 30 -62: 69 type=148 (RBDIHS) 27 26 28 34 -62: 70 type=149 (RBDIHS) 38 26 28 29 -62: 71 type=150 (RBDIHS) 24 26 38 40 -62: 72 type=151 (RBDIHS) 28 26 38 40 -62: 73 type=148 (RBDIHS) 26 28 30 31 -62: 74 type=148 (RBDIHS) 26 28 30 32 -62: 75 type=148 (RBDIHS) 26 28 30 33 -62: 76 type=148 (RBDIHS) 29 28 30 31 -62: 77 type=148 (RBDIHS) 29 28 30 32 -62: 78 type=148 (RBDIHS) 29 28 30 33 -62: 79 type=148 (RBDIHS) 34 28 30 31 -62: 80 type=148 (RBDIHS) 34 28 30 32 -62: 81 type=148 (RBDIHS) 34 28 30 33 -62: 82 type=148 (RBDIHS) 26 28 34 35 -62: 83 type=148 (RBDIHS) 26 28 34 36 -62: 84 type=148 (RBDIHS) 26 28 34 37 -62: 85 type=148 (RBDIHS) 29 28 34 35 -62: 86 type=148 (RBDIHS) 29 28 34 36 -62: 87 type=148 (RBDIHS) 29 28 34 37 -62: 88 type=148 (RBDIHS) 30 28 34 35 -62: 89 type=148 (RBDIHS) 30 28 34 36 -62: 90 type=148 (RBDIHS) 30 28 34 37 -62: 91 type=155 (RBDIHS) 26 38 40 41 -62: 92 type=156 (RBDIHS) 26 38 40 42 -62: 93 type=155 (RBDIHS) 39 38 40 41 -62: 94 type=157 (RBDIHS) 39 38 40 42 -62: 95 type=158 (RBDIHS) 38 40 42 44 -62: 96 type=159 (RBDIHS) 38 40 42 58 -62: 97 type=147 (RBDIHS) 40 42 44 45 -62: 98 type=147 (RBDIHS) 40 42 44 46 -62: 99 type=162 (RBDIHS) 40 42 44 47 -62: 100 type=148 (RBDIHS) 43 42 44 45 -62: 101 type=148 (RBDIHS) 43 42 44 46 -62: 102 type=163 (RBDIHS) 43 42 44 47 -62: 103 type=149 (RBDIHS) 58 42 44 45 -62: 104 type=149 (RBDIHS) 58 42 44 46 -62: 105 type=164 (RBDIHS) 58 42 44 47 -62: 106 type=150 (RBDIHS) 40 42 58 60 -62: 107 type=151 (RBDIHS) 44 42 58 60 -62: 108 type=165 (RBDIHS) 44 47 48 49 -62: 109 type=165 (RBDIHS) 44 47 48 52 -62: 110 type=165 (RBDIHS) 50 47 48 49 -62: 111 type=165 (RBDIHS) 50 47 48 52 -62: 112 type=165 (RBDIHS) 44 47 50 51 -62: 113 type=165 (RBDIHS) 44 47 50 54 -62: 114 type=165 (RBDIHS) 48 47 50 51 -62: 115 type=165 (RBDIHS) 48 47 50 54 -62: 116 type=165 (RBDIHS) 47 48 52 53 -62: 117 type=165 (RBDIHS) 47 48 52 56 -62: 118 type=165 (RBDIHS) 49 48 52 53 -62: 119 type=165 (RBDIHS) 49 48 52 56 -62: 120 type=165 (RBDIHS) 47 50 54 55 -62: 121 type=165 (RBDIHS) 47 50 54 56 -62: 122 type=165 (RBDIHS) 51 50 54 55 -62: 123 type=165 (RBDIHS) 51 50 54 56 -62: 124 type=165 (RBDIHS) 48 52 56 54 -62: 125 type=165 (RBDIHS) 48 52 56 57 -62: 126 type=165 (RBDIHS) 53 52 56 54 -62: 127 type=165 (RBDIHS) 53 52 56 57 -62: 128 type=165 (RBDIHS) 50 54 56 52 -62: 129 type=165 (RBDIHS) 50 54 56 57 -62: 130 type=165 (RBDIHS) 55 54 56 52 -62: 131 type=165 (RBDIHS) 55 54 56 57 -62: 132 type=155 (RBDIHS) 42 58 60 61 -62: 133 type=156 (RBDIHS) 42 58 60 62 -62: 134 type=155 (RBDIHS) 59 58 60 61 -62: 135 type=157 (RBDIHS) 59 58 60 62 -62: 136 type=159 (RBDIHS) 58 60 62 65 -62: 137 type=150 (RBDIHS) 60 62 65 67 -62: 138 type=155 (RBDIHS) 62 65 67 68 -62: 139 type=156 (RBDIHS) 62 65 67 69 -62: 140 type=155 (RBDIHS) 66 65 67 68 -62: 141 type=157 (RBDIHS) 66 65 67 69 -62: 142 type=158 (RBDIHS) 65 67 69 71 -62: 143 type=159 (RBDIHS) 65 67 69 89 -62: 144 type=166 (RBDIHS) 67 69 71 74 -62: 145 type=167 (RBDIHS) 89 69 71 74 -62: 146 type=147 (RBDIHS) 67 69 71 72 -62: 147 type=147 (RBDIHS) 67 69 71 73 -62: 148 type=148 (RBDIHS) 70 69 71 72 -62: 149 type=148 (RBDIHS) 70 69 71 73 -62: 150 type=148 (RBDIHS) 70 69 71 74 -62: 151 type=149 (RBDIHS) 89 69 71 72 -62: 152 type=149 (RBDIHS) 89 69 71 73 -62: 153 type=150 (RBDIHS) 67 69 89 91 -62: 154 type=151 (RBDIHS) 71 69 89 91 -62: 155 type=148 (RBDIHS) 69 71 74 75 -62: 156 type=148 (RBDIHS) 69 71 74 76 -62: 157 type=152 (RBDIHS) 69 71 74 77 -62: 158 type=148 (RBDIHS) 72 71 74 75 -62: 159 type=148 (RBDIHS) 72 71 74 76 -62: 160 type=148 (RBDIHS) 72 71 74 77 -62: 161 type=148 (RBDIHS) 73 71 74 75 -62: 162 type=148 (RBDIHS) 73 71 74 76 -62: 163 type=148 (RBDIHS) 73 71 74 77 -62: 164 type=148 (RBDIHS) 71 74 77 78 -62: 165 type=148 (RBDIHS) 71 74 77 79 -62: 166 type=153 (RBDIHS) 71 74 77 80 -62: 167 type=148 (RBDIHS) 75 74 77 78 -62: 168 type=148 (RBDIHS) 75 74 77 79 -62: 169 type=168 (RBDIHS) 75 74 77 80 -62: 170 type=148 (RBDIHS) 76 74 77 78 -62: 171 type=148 (RBDIHS) 76 74 77 79 -62: 172 type=168 (RBDIHS) 76 74 77 80 -62: 173 type=169 (RBDIHS) 74 77 80 81 -62: 174 type=170 (RBDIHS) 74 77 80 82 -62: 175 type=171 (RBDIHS) 78 77 80 82 -62: 176 type=171 (RBDIHS) 79 77 80 82 -62: 177 type=172 (RBDIHS) 77 80 82 83 -62: 178 type=172 (RBDIHS) 77 80 82 86 -62: 179 type=173 (RBDIHS) 81 80 82 83 -62: 180 type=173 (RBDIHS) 81 80 82 86 -62: 181 type=173 (RBDIHS) 80 82 83 84 -62: 182 type=173 (RBDIHS) 80 82 83 85 -62: 183 type=173 (RBDIHS) 86 82 83 84 -62: 184 type=173 (RBDIHS) 86 82 83 85 -62: 185 type=173 (RBDIHS) 80 82 86 87 -62: 186 type=173 (RBDIHS) 80 82 86 88 -62: 187 type=173 (RBDIHS) 83 82 86 87 -62: 188 type=173 (RBDIHS) 83 82 86 88 -62: 189 type=155 (RBDIHS) 69 89 91 92 -62: 190 type=156 (RBDIHS) 69 89 91 93 -62: 191 type=155 (RBDIHS) 90 89 91 92 -62: 192 type=157 (RBDIHS) 90 89 91 93 -62: 193 type=158 (RBDIHS) 89 91 93 95 -62: 194 type=159 (RBDIHS) 89 91 93 100 -62: 195 type=174 (RBDIHS) 91 93 95 98 -62: 196 type=175 (RBDIHS) 100 93 95 98 -62: 197 type=147 (RBDIHS) 91 93 95 96 -62: 198 type=147 (RBDIHS) 91 93 95 97 -62: 199 type=148 (RBDIHS) 94 93 95 96 -62: 200 type=148 (RBDIHS) 94 93 95 97 -62: 201 type=176 (RBDIHS) 94 93 95 98 -62: 202 type=149 (RBDIHS) 100 93 95 96 -62: 203 type=149 (RBDIHS) 100 93 95 97 -62: 204 type=150 (RBDIHS) 91 93 100 102 -62: 205 type=151 (RBDIHS) 95 93 100 102 -62: 206 type=177 (RBDIHS) 93 95 98 99 -62: 207 type=178 (RBDIHS) 96 95 98 99 -62: 208 type=178 (RBDIHS) 97 95 98 99 -62: 209 type=155 (RBDIHS) 93 100 102 103 -62: 210 type=156 (RBDIHS) 93 100 102 104 -62: 211 type=155 (RBDIHS) 101 100 102 103 -62: 212 type=157 (RBDIHS) 101 100 102 104 -62: 213 type=158 (RBDIHS) 100 102 104 106 -62: 214 type=159 (RBDIHS) 100 102 104 115 -62: 215 type=179 (RBDIHS) 102 104 106 109 -62: 216 type=180 (RBDIHS) 115 104 106 109 -62: 217 type=147 (RBDIHS) 102 104 106 107 -62: 218 type=147 (RBDIHS) 102 104 106 108 -62: 219 type=148 (RBDIHS) 105 104 106 107 -62: 220 type=148 (RBDIHS) 105 104 106 108 -62: 221 type=148 (RBDIHS) 105 104 106 109 -62: 222 type=149 (RBDIHS) 115 104 106 107 -62: 223 type=149 (RBDIHS) 115 104 106 108 -62: 224 type=150 (RBDIHS) 102 104 115 117 -62: 225 type=151 (RBDIHS) 106 104 115 117 -62: 226 type=148 (RBDIHS) 104 106 109 110 -62: 227 type=148 (RBDIHS) 104 106 109 111 -62: 228 type=181 (RBDIHS) 104 106 109 112 -62: 229 type=148 (RBDIHS) 107 106 109 110 -62: 230 type=148 (RBDIHS) 107 106 109 111 -62: 231 type=182 (RBDIHS) 107 106 109 112 -62: 232 type=148 (RBDIHS) 108 106 109 110 -62: 233 type=148 (RBDIHS) 108 106 109 111 -62: 234 type=182 (RBDIHS) 108 106 109 112 -62: 235 type=183 (RBDIHS) 106 109 112 113 -62: 236 type=183 (RBDIHS) 106 109 112 114 -62: 237 type=155 (RBDIHS) 104 115 117 118 -62: 238 type=156 (RBDIHS) 104 115 117 119 -62: 239 type=155 (RBDIHS) 116 115 117 118 -62: 240 type=157 (RBDIHS) 116 115 117 119 -62: 241 type=158 (RBDIHS) 115 117 119 121 -62: 242 type=159 (RBDIHS) 115 117 119 134 -62: 243 type=184 (RBDIHS) 117 119 121 124 -62: 244 type=185 (RBDIHS) 134 119 121 124 -62: 245 type=147 (RBDIHS) 117 119 121 122 -62: 246 type=147 (RBDIHS) 117 119 121 123 -62: 247 type=148 (RBDIHS) 120 119 121 122 -62: 248 type=148 (RBDIHS) 120 119 121 123 -62: 249 type=148 (RBDIHS) 120 119 121 124 -62: 250 type=149 (RBDIHS) 134 119 121 122 -62: 251 type=149 (RBDIHS) 134 119 121 123 -62: 252 type=150 (RBDIHS) 117 119 134 136 -62: 253 type=151 (RBDIHS) 121 119 134 136 -62: 254 type=148 (RBDIHS) 119 121 124 125 -62: 255 type=152 (RBDIHS) 119 121 124 126 -62: 256 type=152 (RBDIHS) 119 121 124 130 -62: 257 type=148 (RBDIHS) 122 121 124 125 -62: 258 type=148 (RBDIHS) 122 121 124 126 -62: 259 type=148 (RBDIHS) 122 121 124 130 -62: 260 type=148 (RBDIHS) 123 121 124 125 -62: 261 type=148 (RBDIHS) 123 121 124 126 -62: 262 type=148 (RBDIHS) 123 121 124 130 -62: 263 type=148 (RBDIHS) 121 124 126 127 -62: 264 type=148 (RBDIHS) 121 124 126 128 -62: 265 type=148 (RBDIHS) 121 124 126 129 -62: 266 type=148 (RBDIHS) 125 124 126 127 -62: 267 type=148 (RBDIHS) 125 124 126 128 -62: 268 type=148 (RBDIHS) 125 124 126 129 -62: 269 type=148 (RBDIHS) 130 124 126 127 -62: 270 type=148 (RBDIHS) 130 124 126 128 -62: 271 type=148 (RBDIHS) 130 124 126 129 -62: 272 type=148 (RBDIHS) 121 124 130 131 -62: 273 type=148 (RBDIHS) 121 124 130 132 -62: 274 type=148 (RBDIHS) 121 124 130 133 -62: 275 type=148 (RBDIHS) 125 124 130 131 -62: 276 type=148 (RBDIHS) 125 124 130 132 -62: 277 type=148 (RBDIHS) 125 124 130 133 -62: 278 type=148 (RBDIHS) 126 124 130 131 -62: 279 type=148 (RBDIHS) 126 124 130 132 -62: 280 type=148 (RBDIHS) 126 124 130 133 -62: 281 type=155 (RBDIHS) 119 134 136 137 -62: 282 type=156 (RBDIHS) 119 134 136 138 -62: 283 type=155 (RBDIHS) 135 134 136 137 -62: 284 type=157 (RBDIHS) 135 134 136 138 -62: 285 type=158 (RBDIHS) 134 136 138 140 -62: 286 type=159 (RBDIHS) 134 136 138 144 -62: 287 type=147 (RBDIHS) 136 138 140 141 -62: 288 type=147 (RBDIHS) 136 138 140 142 -62: 289 type=147 (RBDIHS) 136 138 140 143 -62: 290 type=148 (RBDIHS) 139 138 140 141 -62: 291 type=148 (RBDIHS) 139 138 140 142 -62: 292 type=148 (RBDIHS) 139 138 140 143 -62: 293 type=149 (RBDIHS) 144 138 140 141 -62: 294 type=149 (RBDIHS) 144 138 140 142 -62: 295 type=149 (RBDIHS) 144 138 140 143 -62: 296 type=150 (RBDIHS) 136 138 144 146 -62: 297 type=151 (RBDIHS) 140 138 144 146 -62: 298 type=155 (RBDIHS) 138 144 146 147 -62: 299 type=156 (RBDIHS) 138 144 146 148 -62: 300 type=155 (RBDIHS) 145 144 146 147 -62: 301 type=157 (RBDIHS) 145 144 146 148 -62: 302 type=158 (RBDIHS) 144 146 148 150 -62: 303 type=159 (RBDIHS) 144 146 148 154 -62: 304 type=147 (RBDIHS) 146 148 150 151 -62: 305 type=147 (RBDIHS) 146 148 150 152 -62: 306 type=147 (RBDIHS) 146 148 150 153 -62: 307 type=148 (RBDIHS) 149 148 150 151 -62: 308 type=148 (RBDIHS) 149 148 150 152 -62: 309 type=148 (RBDIHS) 149 148 150 153 -62: 310 type=149 (RBDIHS) 154 148 150 151 -62: 311 type=149 (RBDIHS) 154 148 150 152 -62: 312 type=149 (RBDIHS) 154 148 150 153 -62: Restr. Dih.: -62: nr: 0 -62: CBT Dih.: -62: nr: 0 -62: Fourier Dih.: -62: nr: 0 -62: Improper Dih.: -62: nr: 0 -62: Per. Imp. Dih.: -62: nr: 0 -62: Tab. Dih.: -62: nr: 0 -62: CMAP Dih.: -62: nr: 0 -62: GB 1-2 Pol.: -62: nr: 0 -62: GB 1-3 Pol.: -62: nr: 0 -62: GB 1-4 Pol.: -62: nr: 0 -62: GB Polariz.: -62: nr: 0 -62: Nonpolar Sol.: -62: nr: 0 -62: LJ-14: -62: nr: 1197 -62: iatoms: -62: 0 type=186 (LJ14) 0 7 -62: 1 type=186 (LJ14) 0 8 -62: 2 type=187 (LJ14) 0 9 -62: 3 type=188 (LJ14) 0 23 -62: 4 type=189 (LJ14) 0 24 -62: 5 type=190 (LJ14) 1 5 -62: 6 type=190 (LJ14) 1 6 -62: 7 type=190 (LJ14) 1 22 -62: 8 type=190 (LJ14) 2 5 -62: 9 type=190 (LJ14) 2 6 -62: 10 type=190 (LJ14) 2 22 -62: 11 type=190 (LJ14) 3 5 -62: 12 type=190 (LJ14) 3 6 -62: 13 type=190 (LJ14) 3 22 -62: 14 type=191 (LJ14) 4 10 -62: 15 type=191 (LJ14) 4 11 -62: 16 type=192 (LJ14) 4 12 -62: 17 type=190 (LJ14) 4 25 -62: 18 type=192 (LJ14) 4 26 -62: 19 type=193 (LJ14) 5 7 -62: 20 type=193 (LJ14) 5 8 -62: 21 type=191 (LJ14) 5 9 -62: 22 type=194 (LJ14) 5 23 -62: 23 type=186 (LJ14) 5 24 -62: 24 type=191 (LJ14) 6 13 -62: 25 type=191 (LJ14) 6 14 -62: 26 type=192 (LJ14) 6 15 -62: 27 type=195 (LJ14) 6 23 -62: 28 type=187 (LJ14) 6 24 -62: 29 type=193 (LJ14) 7 10 -62: 30 type=193 (LJ14) 7 11 -62: 31 type=191 (LJ14) 7 12 -62: 32 type=196 (LJ14) 7 22 -62: 33 type=193 (LJ14) 8 10 -62: 34 type=193 (LJ14) 8 11 -62: 35 type=191 (LJ14) 8 12 -62: 36 type=196 (LJ14) 8 22 -62: 37 type=191 (LJ14) 9 16 -62: 38 type=191 (LJ14) 9 17 -62: 39 type=187 (LJ14) 9 18 -62: 40 type=197 (LJ14) 9 22 -62: 41 type=193 (LJ14) 10 13 -62: 42 type=193 (LJ14) 10 14 -62: 43 type=191 (LJ14) 10 15 -62: 44 type=193 (LJ14) 11 13 -62: 45 type=193 (LJ14) 11 14 -62: 46 type=191 (LJ14) 11 15 -62: 47 type=190 (LJ14) 12 19 -62: 48 type=190 (LJ14) 12 20 -62: 49 type=190 (LJ14) 12 21 -62: 50 type=193 (LJ14) 13 16 -62: 51 type=193 (LJ14) 13 17 -62: 52 type=186 (LJ14) 13 18 -62: 53 type=193 (LJ14) 14 16 -62: 54 type=193 (LJ14) 14 17 -62: 55 type=186 (LJ14) 14 18 -62: 56 type=190 (LJ14) 16 19 -62: 57 type=190 (LJ14) 16 20 -62: 58 type=190 (LJ14) 16 21 -62: 59 type=190 (LJ14) 17 19 -62: 60 type=190 (LJ14) 17 20 -62: 61 type=190 (LJ14) 17 21 -62: 62 type=196 (LJ14) 22 27 -62: 63 type=197 (LJ14) 22 28 -62: 64 type=198 (LJ14) 22 38 -62: 65 type=190 (LJ14) 23 25 -62: 66 type=195 (LJ14) 23 26 -62: 67 type=186 (LJ14) 24 29 -62: 68 type=187 (LJ14) 24 30 -62: 69 type=187 (LJ14) 24 34 -62: 70 type=188 (LJ14) 24 39 -62: 71 type=189 (LJ14) 24 40 -62: 72 type=190 (LJ14) 25 27 -62: 73 type=190 (LJ14) 25 28 -62: 74 type=190 (LJ14) 25 38 -62: 75 type=191 (LJ14) 26 31 -62: 76 type=191 (LJ14) 26 32 -62: 77 type=191 (LJ14) 26 33 -62: 78 type=191 (LJ14) 26 35 -62: 79 type=191 (LJ14) 26 36 -62: 80 type=191 (LJ14) 26 37 -62: 81 type=190 (LJ14) 26 41 -62: 82 type=192 (LJ14) 26 42 -62: 83 type=193 (LJ14) 27 29 -62: 84 type=191 (LJ14) 27 30 -62: 85 type=191 (LJ14) 27 34 -62: 86 type=194 (LJ14) 27 39 -62: 87 type=186 (LJ14) 27 40 -62: 88 type=195 (LJ14) 28 39 -62: 89 type=187 (LJ14) 28 40 -62: 90 type=193 (LJ14) 29 31 -62: 91 type=193 (LJ14) 29 32 -62: 92 type=193 (LJ14) 29 33 -62: 93 type=193 (LJ14) 29 35 -62: 94 type=193 (LJ14) 29 36 -62: 95 type=193 (LJ14) 29 37 -62: 96 type=196 (LJ14) 29 38 -62: 97 type=191 (LJ14) 30 35 -62: 98 type=191 (LJ14) 30 36 -62: 99 type=191 (LJ14) 30 37 -62: 100 type=197 (LJ14) 30 38 -62: 101 type=191 (LJ14) 31 34 -62: 102 type=191 (LJ14) 32 34 -62: 103 type=191 (LJ14) 33 34 -62: 104 type=197 (LJ14) 34 38 -62: 105 type=196 (LJ14) 38 43 -62: 106 type=197 (LJ14) 38 44 -62: 107 type=198 (LJ14) 38 58 -62: 108 type=190 (LJ14) 39 41 -62: 109 type=195 (LJ14) 39 42 -62: 110 type=186 (LJ14) 40 45 -62: 111 type=186 (LJ14) 40 46 -62: 112 type=199 (LJ14) 40 47 -62: 113 type=188 (LJ14) 40 59 -62: 114 type=189 (LJ14) 40 60 -62: 115 type=190 (LJ14) 41 43 -62: 116 type=190 (LJ14) 41 44 -62: 117 type=190 (LJ14) 41 58 -62: 118 type=200 (LJ14) 42 48 -62: 119 type=200 (LJ14) 42 50 -62: 120 type=190 (LJ14) 42 61 -62: 121 type=192 (LJ14) 42 62 -62: 122 type=193 (LJ14) 43 45 -62: 123 type=193 (LJ14) 43 46 -62: 124 type=201 (LJ14) 43 47 -62: 125 type=194 (LJ14) 43 59 -62: 126 type=186 (LJ14) 43 60 -62: 127 type=202 (LJ14) 44 49 -62: 128 type=202 (LJ14) 44 51 -62: 129 type=200 (LJ14) 44 52 -62: 130 type=200 (LJ14) 44 54 -62: 131 type=195 (LJ14) 44 59 -62: 132 type=187 (LJ14) 44 60 -62: 133 type=201 (LJ14) 45 48 -62: 134 type=201 (LJ14) 45 50 -62: 135 type=196 (LJ14) 45 58 -62: 136 type=201 (LJ14) 46 48 -62: 137 type=201 (LJ14) 46 50 -62: 138 type=196 (LJ14) 46 58 -62: 139 type=203 (LJ14) 47 53 -62: 140 type=203 (LJ14) 47 55 -62: 141 type=204 (LJ14) 47 56 -62: 142 type=205 (LJ14) 47 58 -62: 143 type=203 (LJ14) 48 51 -62: 144 type=204 (LJ14) 48 54 -62: 145 type=203 (LJ14) 48 57 -62: 146 type=203 (LJ14) 49 50 -62: 147 type=206 (LJ14) 49 53 -62: 148 type=203 (LJ14) 49 56 -62: 149 type=204 (LJ14) 50 52 -62: 150 type=203 (LJ14) 50 57 -62: 151 type=206 (LJ14) 51 55 -62: 152 type=203 (LJ14) 51 56 -62: 153 type=203 (LJ14) 52 55 -62: 154 type=203 (LJ14) 53 54 -62: 155 type=206 (LJ14) 53 57 -62: 156 type=206 (LJ14) 55 57 -62: 157 type=196 (LJ14) 58 63 -62: 158 type=196 (LJ14) 58 64 -62: 159 type=198 (LJ14) 58 65 -62: 160 type=190 (LJ14) 59 61 -62: 161 type=195 (LJ14) 59 62 -62: 162 type=188 (LJ14) 60 66 -62: 163 type=189 (LJ14) 60 67 -62: 164 type=190 (LJ14) 61 63 -62: 165 type=190 (LJ14) 61 64 -62: 166 type=190 (LJ14) 61 65 -62: 167 type=190 (LJ14) 62 68 -62: 168 type=192 (LJ14) 62 69 -62: 169 type=194 (LJ14) 63 66 -62: 170 type=186 (LJ14) 63 67 -62: 171 type=194 (LJ14) 64 66 -62: 172 type=186 (LJ14) 64 67 -62: 173 type=196 (LJ14) 65 70 -62: 174 type=197 (LJ14) 65 71 -62: 175 type=198 (LJ14) 65 89 -62: 176 type=190 (LJ14) 66 68 -62: 177 type=195 (LJ14) 66 69 -62: 178 type=186 (LJ14) 67 72 -62: 179 type=186 (LJ14) 67 73 -62: 180 type=187 (LJ14) 67 74 -62: 181 type=188 (LJ14) 67 90 -62: 182 type=189 (LJ14) 67 91 -62: 183 type=190 (LJ14) 68 70 -62: 184 type=190 (LJ14) 68 71 -62: 185 type=190 (LJ14) 68 89 -62: 186 type=191 (LJ14) 69 75 -62: 187 type=191 (LJ14) 69 76 -62: 188 type=192 (LJ14) 69 77 -62: 189 type=190 (LJ14) 69 92 -62: 190 type=192 (LJ14) 69 93 -62: 191 type=193 (LJ14) 70 72 -62: 192 type=193 (LJ14) 70 73 -62: 193 type=191 (LJ14) 70 74 -62: 194 type=194 (LJ14) 70 90 -62: 195 type=186 (LJ14) 70 91 -62: 196 type=191 (LJ14) 71 78 -62: 197 type=191 (LJ14) 71 79 -62: 198 type=187 (LJ14) 71 80 -62: 199 type=195 (LJ14) 71 90 -62: 200 type=187 (LJ14) 71 91 -62: 201 type=193 (LJ14) 72 75 -62: 202 type=193 (LJ14) 72 76 -62: 203 type=191 (LJ14) 72 77 -62: 204 type=196 (LJ14) 72 89 -62: 205 type=193 (LJ14) 73 75 -62: 206 type=193 (LJ14) 73 76 -62: 207 type=191 (LJ14) 73 77 -62: 208 type=196 (LJ14) 73 89 -62: 209 type=190 (LJ14) 74 81 -62: 210 type=207 (LJ14) 74 82 -62: 211 type=197 (LJ14) 74 89 -62: 212 type=193 (LJ14) 75 78 -62: 213 type=193 (LJ14) 75 79 -62: 214 type=186 (LJ14) 75 80 -62: 215 type=193 (LJ14) 76 78 -62: 216 type=193 (LJ14) 76 79 -62: 217 type=186 (LJ14) 76 80 -62: 218 type=187 (LJ14) 77 83 -62: 219 type=187 (LJ14) 77 86 -62: 220 type=190 (LJ14) 78 81 -62: 221 type=208 (LJ14) 78 82 -62: 222 type=190 (LJ14) 79 81 -62: 223 type=208 (LJ14) 79 82 -62: 224 type=190 (LJ14) 80 84 -62: 225 type=190 (LJ14) 80 85 -62: 226 type=190 (LJ14) 80 87 -62: 227 type=190 (LJ14) 80 88 -62: 228 type=190 (LJ14) 81 83 -62: 229 type=190 (LJ14) 81 86 -62: 230 type=190 (LJ14) 83 87 -62: 231 type=190 (LJ14) 83 88 -62: 232 type=190 (LJ14) 84 86 -62: 233 type=190 (LJ14) 85 86 -62: 234 type=196 (LJ14) 89 94 -62: 235 type=197 (LJ14) 89 95 -62: 236 type=198 (LJ14) 89 100 -62: 237 type=190 (LJ14) 90 92 -62: 238 type=195 (LJ14) 90 93 -62: 239 type=186 (LJ14) 91 96 -62: 240 type=186 (LJ14) 91 97 -62: 241 type=209 (LJ14) 91 98 -62: 242 type=188 (LJ14) 91 101 -62: 243 type=189 (LJ14) 91 102 -62: 244 type=190 (LJ14) 92 94 -62: 245 type=190 (LJ14) 92 95 -62: 246 type=190 (LJ14) 92 100 -62: 247 type=190 (LJ14) 93 99 -62: 248 type=190 (LJ14) 93 103 -62: 249 type=192 (LJ14) 93 104 -62: 250 type=193 (LJ14) 94 96 -62: 251 type=193 (LJ14) 94 97 -62: 252 type=210 (LJ14) 94 98 -62: 253 type=194 (LJ14) 94 101 -62: 254 type=186 (LJ14) 94 102 -62: 255 type=195 (LJ14) 95 101 -62: 256 type=187 (LJ14) 95 102 -62: 257 type=190 (LJ14) 96 99 -62: 258 type=196 (LJ14) 96 100 -62: 259 type=190 (LJ14) 97 99 -62: 260 type=196 (LJ14) 97 100 -62: 261 type=211 (LJ14) 98 100 -62: 262 type=196 (LJ14) 100 105 -62: 263 type=197 (LJ14) 100 106 -62: 264 type=198 (LJ14) 100 115 -62: 265 type=190 (LJ14) 101 103 -62: 266 type=195 (LJ14) 101 104 -62: 267 type=186 (LJ14) 102 107 -62: 268 type=186 (LJ14) 102 108 -62: 269 type=187 (LJ14) 102 109 -62: 270 type=188 (LJ14) 102 116 -62: 271 type=189 (LJ14) 102 117 -62: 272 type=190 (LJ14) 103 105 -62: 273 type=190 (LJ14) 103 106 -62: 274 type=190 (LJ14) 103 115 -62: 275 type=191 (LJ14) 104 110 -62: 276 type=191 (LJ14) 104 111 -62: 277 type=197 (LJ14) 104 112 -62: 278 type=190 (LJ14) 104 118 -62: 279 type=192 (LJ14) 104 119 -62: 280 type=193 (LJ14) 105 107 -62: 281 type=193 (LJ14) 105 108 -62: 282 type=191 (LJ14) 105 109 -62: 283 type=194 (LJ14) 105 116 -62: 284 type=186 (LJ14) 105 117 -62: 285 type=195 (LJ14) 106 113 -62: 286 type=195 (LJ14) 106 114 -62: 287 type=195 (LJ14) 106 116 -62: 288 type=187 (LJ14) 106 117 -62: 289 type=193 (LJ14) 107 110 -62: 290 type=193 (LJ14) 107 111 -62: 291 type=196 (LJ14) 107 112 -62: 292 type=196 (LJ14) 107 115 -62: 293 type=193 (LJ14) 108 110 -62: 294 type=193 (LJ14) 108 111 -62: 295 type=196 (LJ14) 108 112 -62: 296 type=196 (LJ14) 108 115 -62: 297 type=197 (LJ14) 109 115 -62: 298 type=194 (LJ14) 110 113 -62: 299 type=194 (LJ14) 110 114 -62: 300 type=194 (LJ14) 111 113 -62: 301 type=194 (LJ14) 111 114 -62: 302 type=196 (LJ14) 115 120 -62: 303 type=197 (LJ14) 115 121 -62: 304 type=198 (LJ14) 115 134 -62: 305 type=190 (LJ14) 116 118 -62: 306 type=195 (LJ14) 116 119 -62: 307 type=186 (LJ14) 117 122 -62: 308 type=186 (LJ14) 117 123 -62: 309 type=187 (LJ14) 117 124 -62: 310 type=188 (LJ14) 117 135 -62: 311 type=189 (LJ14) 117 136 -62: 312 type=190 (LJ14) 118 120 -62: 313 type=190 (LJ14) 118 121 -62: 314 type=190 (LJ14) 118 134 -62: 315 type=191 (LJ14) 119 125 -62: 316 type=192 (LJ14) 119 126 -62: 317 type=192 (LJ14) 119 130 -62: 318 type=190 (LJ14) 119 137 -62: 319 type=192 (LJ14) 119 138 -62: 320 type=193 (LJ14) 120 122 -62: 321 type=193 (LJ14) 120 123 -62: 322 type=191 (LJ14) 120 124 -62: 323 type=194 (LJ14) 120 135 -62: 324 type=186 (LJ14) 120 136 -62: 325 type=191 (LJ14) 121 127 -62: 326 type=191 (LJ14) 121 128 -62: 327 type=191 (LJ14) 121 129 -62: 328 type=191 (LJ14) 121 131 -62: 329 type=191 (LJ14) 121 132 -62: 330 type=191 (LJ14) 121 133 -62: 331 type=195 (LJ14) 121 135 -62: 332 type=187 (LJ14) 121 136 -62: 333 type=193 (LJ14) 122 125 -62: 334 type=191 (LJ14) 122 126 -62: 335 type=191 (LJ14) 122 130 -62: 336 type=196 (LJ14) 122 134 -62: 337 type=193 (LJ14) 123 125 -62: 338 type=191 (LJ14) 123 126 -62: 339 type=191 (LJ14) 123 130 -62: 340 type=196 (LJ14) 123 134 -62: 341 type=197 (LJ14) 124 134 -62: 342 type=193 (LJ14) 125 127 -62: 343 type=193 (LJ14) 125 128 -62: 344 type=193 (LJ14) 125 129 -62: 345 type=193 (LJ14) 125 131 -62: 346 type=193 (LJ14) 125 132 -62: 347 type=193 (LJ14) 125 133 -62: 348 type=191 (LJ14) 126 131 -62: 349 type=191 (LJ14) 126 132 -62: 350 type=191 (LJ14) 126 133 -62: 351 type=191 (LJ14) 127 130 -62: 352 type=191 (LJ14) 128 130 -62: 353 type=191 (LJ14) 129 130 -62: 354 type=196 (LJ14) 134 139 -62: 355 type=197 (LJ14) 134 140 -62: 356 type=198 (LJ14) 134 144 -62: 357 type=190 (LJ14) 135 137 -62: 358 type=195 (LJ14) 135 138 -62: 359 type=186 (LJ14) 136 141 -62: 360 type=186 (LJ14) 136 142 -62: 361 type=186 (LJ14) 136 143 -62: 362 type=188 (LJ14) 136 145 -62: 363 type=189 (LJ14) 136 146 -62: 364 type=190 (LJ14) 137 139 -62: 365 type=190 (LJ14) 137 140 -62: 366 type=190 (LJ14) 137 144 -62: 367 type=190 (LJ14) 138 147 -62: 368 type=192 (LJ14) 138 148 -62: 369 type=193 (LJ14) 139 141 -62: 370 type=193 (LJ14) 139 142 -62: 371 type=193 (LJ14) 139 143 -62: 372 type=194 (LJ14) 139 145 -62: 373 type=186 (LJ14) 139 146 -62: 374 type=195 (LJ14) 140 145 -62: 375 type=187 (LJ14) 140 146 -62: 376 type=196 (LJ14) 141 144 -62: 377 type=196 (LJ14) 142 144 -62: 378 type=196 (LJ14) 143 144 -62: 379 type=196 (LJ14) 144 149 -62: 380 type=197 (LJ14) 144 150 -62: 381 type=198 (LJ14) 144 154 -62: 382 type=190 (LJ14) 145 147 -62: 383 type=195 (LJ14) 145 148 -62: 384 type=186 (LJ14) 146 151 -62: 385 type=186 (LJ14) 146 152 -62: 386 type=186 (LJ14) 146 153 -62: 387 type=188 (LJ14) 146 155 -62: 388 type=190 (LJ14) 147 149 -62: 389 type=190 (LJ14) 147 150 -62: 390 type=190 (LJ14) 147 154 -62: 391 type=193 (LJ14) 149 151 -62: 392 type=193 (LJ14) 149 152 -62: 393 type=193 (LJ14) 149 153 -62: 394 type=194 (LJ14) 149 155 -62: 395 type=195 (LJ14) 150 155 -62: 396 type=196 (LJ14) 151 154 -62: 397 type=196 (LJ14) 152 154 -62: 398 type=196 (LJ14) 153 154 -62: Coulomb-14: -62: nr: 0 -62: LJC-14 q: -62: nr: 0 -62: LJC Pairs NB: -62: nr: 0 -62: LJ (SR): -62: nr: 0 -62: Buck.ham (SR): -62: nr: 0 -62: LJ: -62: nr: 0 -62: B.ham: -62: nr: 0 -62: Disper. corr.: -62: nr: 0 -62: Coulomb (SR): -62: nr: 0 -62: Coul: -62: nr: 0 -62: RF excl.: -62: nr: 0 -62: Coul. recip.: -62: nr: 0 -62: LJ recip.: -62: nr: 0 -62: DPD: -62: nr: 0 -62: Polarization: -62: nr: 0 -62: Water Pol.: -62: nr: 0 -62: Thole Pol.: -62: nr: 0 -62: Anharm. Pol.: -62: nr: 0 -62: Position Rest.: -62: nr: 0 -62: Flat-b. P-R.: -62: nr: 0 -62: Dis. Rest.: -62: nr: 0 -62: D.R.Viol. (nm): -62: nr: 0 -62: Orient. Rest.: -62: nr: 0 -62: Ori. R. RMSD: -62: nr: 0 -62: Angle Rest.: -62: nr: 0 -62: Angle Rest. Z: -62: nr: 0 -62: Dih. Rest.: -62: nr: 0 -62: Dih. Rest. Vi.: -62: nr: 0 -62: Constraint: -62: nr: 0 -62: Constr. No Co.: -62: nr: 0 -62: Settle: -62: nr: 0 -62: Virtual site 1: -62: nr: 0 -62: Virtual site 2: -62: nr: 0 -62: Virt. site 2fd: -62: nr: 0 -62: Virtual site 3: -62: nr: 0 -62: Virt. site 3fd: -62: nr: 0 -62: Vir. site 3fad: -62: nr: 0 -62: Vir. site 3out: -62: nr: 0 -62: Virt. site 4fd: -62: nr: 0 -62: Vir. site 4fdn: -62: nr: 0 -62: Virtual site N: -62: nr: 0 -62: COM Pull En.: -62: nr: 0 -62: Dens. fitting: -62: nr: 0 -62: Quantum En.: -62: nr: 0 -62: NN Potential: -62: nr: 0 -62: Potential: -62: nr: 0 -62: Kinetic En.: -62: nr: 0 -62: Total Energy: -62: nr: 0 -62: Conserved En.: -62: nr: 0 -62: Temperature: -62: nr: 0 -62: Vir. Temp.: -62: nr: 0 -62: Pres. DC: -62: nr: 0 -62: Pressure: -62: nr: 0 -62: dH/dl constr.: -62: nr: 0 -62: dVremain/dl: -62: nr: 0 -62: dEkin/dl: -62: nr: 0 -62: dVcoul/dl: -62: nr: 0 -62: dVvdw/dl: -62: nr: 0 -62: dVbonded/dl: -62: nr: 0 -62: dVrestraint/dl: -62: nr: 0 -62: dVtemp/dl: -62: nr: 0 -62: grp[T-Coupling ] nr=1, name=[ rest] -62: grp[Energy Mon. ] nr=1, name=[ rest] -62: grp[Acc. not used] nr=1, name=[ rest] -62: grp[Freeze ] nr=1, name=[ rest] -62: grp[User1 ] nr=1, name=[ rest] -62: grp[User2 ] nr=1, name=[ rest] -62: grp[VCM ] nr=1, name=[ rest] -62: grp[Compressed X] nr=1, name=[ rest] -62: grp[Or. Res. Fit] nr=1, name=[ rest] -62: grp[QMMM ] nr=1, name=[ rest] -62: grpname (11): -62: grpname[0]={name="System"} -62: grpname[1]={name="Protein"} -62: grpname[2]={name="Protein-H"} -62: grpname[3]={name="C-alpha"} -62: grpname[4]={name="Backbone"} -62: grpname[5]={name="MainChain"} -62: grpname[6]={name="MainChain+Cb"} -62: grpname[7]={name="MainChain+H"} -62: grpname[8]={name="SideChain"} -62: grpname[9]={name="SideChain-H"} -62: grpname[10]={name="rest"} -62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM -62: allocated 0 0 0 0 0 0 0 0 0 0 -62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 -62: box (3x3): -62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} -62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} -62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} -62: box_rel (3x3): -62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv (3x3): -62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev (3x3): -62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev (3x3): -62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev (3x3): -62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: nosehoover_xi: not available -62: x (156x3): -62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} -62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} -62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} -62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} -62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} -62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} -62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} -62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} -62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} -62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} -62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} -62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} -62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} -62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} -62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} -62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} -62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} -62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} -62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} -62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} -62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} -62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} -62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} -62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} -62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} -62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} -62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} -62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} -62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} -62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} -62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} -62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} -62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} -62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} -62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} -62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} -62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} -62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} -62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} -62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} -62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} -62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} -62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} -62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} -62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} -62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} -62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} -62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} -62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} -62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} -62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} -62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} -62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} -62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} -62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} -62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} -62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} -62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} -62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} -62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} -62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} -62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} -62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} -62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} -62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} -62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} -62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} -62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} -62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} -62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} -62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} -62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} -62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} -62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} -62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} -62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} -62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} -62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} -62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} -62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} -62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} -62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} -62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} -62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} -62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} -62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} -62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} -62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} -62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} -62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} -62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} -62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} -62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} -62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} -62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} -62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} -62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} -62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} -62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} -62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} -62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} -62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} -62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} -62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} -62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} -62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} -62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} -62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} -62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} -62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} -62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} -62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} -62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} -62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} -62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} -62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} -62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} -62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} -62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} -62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} -62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} -62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} -62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} -62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} -62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} -62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} -62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} -62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} -62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} -62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} -62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} -62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} -62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} -62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} -62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} -62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} -62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} -62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} -62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} -62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} -62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} -62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} -62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} -62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} -62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} -62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} -62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} -62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} -62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} -62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} -62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} -62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} -62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} -62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} -62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} -62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} -62: v (156x3): -62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -62: Group statistics -62: T-Coupling : 156 (total 156 atoms) -62: Energy Mon. : 156 (total 156 atoms) -62: Acc. not used: 156 (total 156 atoms) -62: Freeze : 156 (total 156 atoms) -62: User1 : 156 (total 156 atoms) -62: User2 : 156 (total 156 atoms) -62: VCM : 156 (total 156 atoms) -62: Compressed X: 156 (total 156 atoms) -62: Or. Res. Fit: 156 (total 156 atoms) -62: QMMM : 156 (total 156 atoms) -62: [ OK ] DumpTest.WorksWithTpr (7 ms) -62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) -62: [----------] 2 tests from DumpTest (8 ms total) -62: -62: [----------] 3 tests from HelpwritingTest -62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp -62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) -62: [ RUN ] HelpwritingTest.DumpWritesHelp -62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) -62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp -62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) -62: [----------] 3 tests from HelpwritingTest (0 ms total) -62: -62: [----------] 7 tests from GmxMakeNdx -62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 16 Protein residues -62: Analysing Protein... -62: -62: 0 System : 256 atoms -62: 1 Protein : 256 atoms -62: 2 Protein-H : 139 atoms -62: 3 C-alpha : 16 atoms -62: 4 Backbone : 48 atoms -62: 5 MainChain : 63 atoms -62: 6 MainChain+Cb : 78 atoms -62: 7 MainChain+H : 81 atoms -62: 8 SideChain : 175 atoms -62: 9 SideChain-H : 76 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) -62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput -62: Going to read 1 old index file(s) -62: Deducing 22 atoms in the system from indices in the index file -62: -62: 0 System : 22 atoms -62: 1 Protein : 22 atoms -62: 2 Protein-H : 10 atoms -62: 3 C-alpha : 1 atoms -62: 4 Backbone : 5 atoms -62: 5 MainChain : 7 atoms -62: 6 MainChain+Cb : 8 atoms -62: 7 MainChain+H : 9 atoms -62: 8 SideChain : 13 atoms -62: 9 SideChain-H : 3 atoms -62: 10 CA : 1 atoms -62: 11 C_&_r_1 : 1 atoms -62: 12 C_&_r_2 : 1 atoms -62: 13 N_&_r_2 : 1 atoms -62: 14 N_&_r_3 : 1 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Copied index group 1 'Protein' -62: Copied index group 2 'Protein-H' -62: Merged two groups with OR: 22 10 -> 22 -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) -62: [ RUN ] GmxMakeNdx.HandlesNotProtein -62: Going to read 1 old index file(s) -62: Deducing 6 atoms in the system from indices in the index file -62: -62: 0 System : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) -62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult -62: Going to read 1 old index file(s) -62: Deducing 22 atoms in the system from indices in the index file -62: -62: 0 System : 22 atoms -62: 1 Protein : 22 atoms -62: 2 Protein-H : 10 atoms -62: 3 C-alpha : 1 atoms -62: 4 Backbone : 5 atoms -62: 5 MainChain : 7 atoms -62: 6 MainChain+Cb : 8 atoms -62: 7 MainChain+H : 9 atoms -62: 8 SideChain : 13 atoms -62: 9 SideChain-H : 3 atoms -62: 10 CA : 1 atoms -62: 11 C_&_r_1 : 1 atoms -62: 12 C_&_r_2 : 1 atoms -62: 13 N_&_r_2 : 1 atoms -62: 14 N_&_r_3 : 1 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Copied index group 4 'Backbone' -62: Copied index group 8 'SideChain' -62: Merged two groups with AND: 5 13 -> 0 -62: Group is empty -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) -62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile -62: Going to read 1 old index file(s) -62: Deducing 6 atoms in the system from indices in the index file -62: -62: 0 System : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Removed group 0 'System' -62: -62: > -62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) -62: [ RUN ] GmxMakeNdx.Splitres -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 2 Water residues -62: -62: 0 System : 6 atoms -62: 1 Water : 6 atoms -62: 2 SOL : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Splitting group 1 'Water' into residues -62: -62: > -62: [ OK ] GmxMakeNdx.Splitres (0 ms) -62: [ RUN ] GmxMakeNdx.Splitat -62: -62: Reading structure file -62: Going to read 0 old index file(s) -62: Analysing residue names: -62: There are: 2 Water residues -62: -62: 0 System : 6 atoms -62: 1 Water : 6 atoms -62: 2 SOL : 6 atoms -62: -62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -62: 'r': residue 'res' nr 'chain' char -62: "name": group 'case': case sensitive 'q': save and quit -62: 'ri': residue index -62: -62: > -62: Splitting group 1 'Water' into atoms -62: -62: > -62: [ OK ] GmxMakeNdx.Splitat (0 ms) -62: [----------] 7 tests from GmxMakeNdx (6 ms total) -62: -62: [----------] 4 tests from ReportMethodsTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Setting the LD random seed to -1115815941 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated -62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) -62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted -62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) -62: [ RUN ] ReportMethodsTest.WritesCorrectInformation -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) -62: [ RUN ] ReportMethodsTest.ToolEndToEndTest -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: section: Methods -62: subsection: Simulation system -62: A system of 1 molecules (156 atoms) was simulated. -62: -62: subsection: Simulation settings -62: A total of 0 ns were simulated with a time step of 1 fs. -62: Neighbor searching was performed every 10 steps. -62: The Cut-off algorithm was used for electrostatic interactions. -62: with a cut-off of 1 nm. -62: A single cut-off of 1.1 nm was used for Van der Waals interactions. -62: [ OK ] ReportMethodsTest.ToolEndToEndTest (2 ms) -62: [----------] 4 tests from ReportMethodsTest (2 ms total) -62: -62: [----------] 4 tests from ConvertTprTest -62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting the LD random seed to 1859383167 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: Extending remaining runtime by 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: Extending remaining runtime by 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 200000 -62: Runtime for the run 200 ps -62: Run end step 200000 -62: Run end time 200 ps -62: -62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (287 ms) -62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting the LD random seed to 2145074623 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: Extending remaining runtime to 100 ps -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 100000 -62: Runtime for the run 100 ps -62: Run end step 100000 -62: Run end time 100 ps -62: -62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (293 ms) -62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting nsteps to 102 -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting the LD random seed to -79954945 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: Input file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 0 -62: Runtime for the run 0 ps -62: Run end step 0 -62: Run end time 0 ps -62: -62: -62: Output file: -62: Run start step 0 -62: Run start time 0 ps -62: Step to be made during run 102 -62: Runtime for the run 0.102 ps -62: Run end step 102 -62: Run end time 0.102 ps -62: -62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (293 ms) -62: [ RUN ] ConvertTprTest.generateVelocitiesTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting the LD random seed to -17170433 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] ConvertTprTest.generateVelocitiesTest (290 ms) -62: [----------] 4 tests from ConvertTprTest (1165 ms total) -62: -62: [----------] 1 test from ConvertTprNoVelocityTest -62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: -62: NOTE 3 [file lysozyme.top, line 1465]: -62: Zero-step energy minimization will alter the coordinates before -62: calculating the energy. If you just want the energy of a single point, -62: try zero-step MD (with unconstrained_start = yes). To do multiple -62: single-point energy evaluations of different configurations of the same -62: topology, use mdrun -rerun. -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -62: Setting the LD random seed to -276889607 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (294 ms) -62: [----------] 1 test from ConvertTprNoVelocityTest (294 ms total) -62: -62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: trr version: GMX_trn_file (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (3 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (3 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (1 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (1 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) -62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 -62: Will write trr: Trajectory in portable xdr format -62: Group 0 ( System) has 6 elements -62: Group 1 (FirstWaterMolecule) has 3 elements -62: Group 2 (SecondWaterMolecule) has 3 elements -62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -62: -> frame 1 time 1.000 -62: Last written: frame 1 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: Select group for output -62: Selected 2: 'SecondWaterMolecule' -62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) -62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (14 ms total) -62: -62: [----------] 30 tests from Works/TrjconvDumpTest -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (3 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -62: Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (1 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -62: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -62: Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (1 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 0 ps -62: -> frame 0 time 0.000 -62: Last written: frame 0 time 0.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (1 ms) -62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 -62: Will write trr: Trajectory in portable xdr format -62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -62: -62: Dumping frame at t= 1 ps -62: -> frame 0 time 1.000 -62: Last written: frame 0 time 1.000 -62: -62: -62: Note that major changes are planned in future for trjconv, to improve usability and utility. -62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (1 ms) -62: [----------] 30 tests from Works/TrjconvDumpTest (20 ms total) -62: -62: [----------] Global test environment tear-down -62: [==========] 63 tests from 8 test suites ran. (2082 ms total) -62: [ PASSED ] 63 tests. -62/92 Test #62: ToolUnitTests ............................. Passed 2.10 sec -test 63 - Start 63: ToolWithLeaksUnitTests - -63: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" -63: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests -63: Test timeout computed to be: 1920 -63: [==========] Running 2 tests from 2 test suites. -63: [----------] Global test environment set-up. -63: [----------] 1 test from ConvertTprTest -63: [ RUN ] ConvertTprTest.selectIndexTest -63: -63: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: For a correct single-point energy evaluation with nsteps = 0, use -63: continuation = yes to avoid constraining the input coordinates. -63: -63: Generating 1-4 interactions: fudge = 0.5 -63: -63: NOTE 2 [file lysozyme.top, line 1465]: -63: System has non-zero total charge: 2.000000 -63: Total charge should normally be an integer. See -63: https://manual.gromacs.org/current/user-guide/floating-point.html -63: for discussion on how close it should be to an integer. -63: -63: -63: -63: Number of degrees of freedom in T-Coupling group rest is 465.00 -63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -63: -63: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: NVE simulation with an initial temperature of zero: will use a Verlet -63: buffer of 10%. Check your energy drift! -63: -63: -63: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -63: You are using a plain Coulomb cut-off, which might produce artifacts. -63: You might want to consider using PME electrostatics. -63: -63: -63: -63: There were 4 NOTEs -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Group 0 ( System) has 156 elements -63: Group 1 ( Protein) has 156 elements -63: Group 2 ( Protein-H) has 75 elements -63: Group 3 ( C-alpha) has 10 elements -63: Group 4 ( Backbone) has 30 elements -63: Group 5 ( MainChain) has 40 elements -63: Group 6 ( MainChain+Cb) has 49 elements -63: Group 7 ( MainChain+H) has 52 elements -63: Group 8 ( SideChain) has 104 elements -63: Group 9 ( SideChain-H) has 35 elements -63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -63: Reduced ilist BONDS from 156 to 75 entries -63: Reduced ilist ANGLES from 281 to 98 entries -63: Reduced ilist PDIHS from 29 to 12 entries -63: Reduced ilist RBDIHS from 313 to 89 entries -63: Reduced ilist LJ14 from 399 to 107 entries -63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Setting the LD random seed to -687878449 -63: -63: Generated 330891 of the 330891 non-bonded parameter combinations -63: -63: Generated 330891 of the 330891 1-4 parameter combinations -63: -63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -63: -63: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -63: Analysing residue names: -63: There are: 10 Protein residues -63: Analysing Protein... -63: -63: This run will generate roughly 0 Mb of data -63: Selected 2: 'Protein-H' -63: [ OK ] ConvertTprTest.selectIndexTest (304 ms) -63: [----------] 1 test from ConvertTprTest (304 ms total) -63: -63: [----------] 1 test from ConvertTprNoVelocityTest -63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity -63: -63: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -63: For a correct single-point energy evaluation with nsteps = 0, use -63: continuation = yes to avoid constraining the input coordinates. -63: -63: Generating 1-4 interactions: fudge = 0.5 -63: -63: NOTE 2 [file lysozyme.top, line 1465]: -63: System has non-zero total charge: 2.000000 -63: Total charge should normally be an integer. See -63: https://manual.gromacs.org/current/user-guide/floating-point.html -63: for discussion on how close it should be to an integer. -63: -63: -63: -63: -63: NOTE 3 [file lysozyme.top, line 1465]: -63: Zero-step energy minimization will alter the coordinates before -63: calculating the energy. If you just want the energy of a single point, -63: try zero-step MD (with unconstrained_start = yes). To do multiple -63: single-point energy evaluations of different configurations of the same -63: topology, use mdrun -rerun. -63: -63: Number of degrees of freedom in T-Coupling group rest is 465.00 -63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -63: -63: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -63: You are using a plain Coulomb cut-off, which might produce artifacts. -63: You might want to consider using PME electrostatics. -63: -63: -63: -63: There were 4 NOTEs -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Group 0 ( System) has 156 elements -63: Group 1 ( Protein) has 156 elements -63: Group 2 ( Protein-H) has 75 elements -63: Group 3 ( C-alpha) has 10 elements -63: Group 4 ( Backbone) has 30 elements -63: Group 5 ( MainChain) has 40 elements -63: Group 6 ( MainChain+Cb) has 49 elements -63: Group 7 ( MainChain+H) has 52 elements -63: Group 8 ( SideChain) has 104 elements -63: Group 9 ( SideChain-H) has 35 elements -63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -63: Reduced ilist BONDS from 156 to 75 entries -63: Reduced ilist ANGLES from 281 to 98 entries -63: Reduced ilist PDIHS from 29 to 12 entries -63: Reduced ilist RBDIHS from 313 to 89 entries -63: Reduced ilist LJ14 from 399 to 107 entries -63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -63: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -63: Setting the LD random seed to -1415078671 -63: -63: Generated 330891 of the 330891 non-bonded parameter combinations -63: -63: Generated 330891 of the 330891 1-4 parameter combinations -63: -63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -63: Analysing residue names: -63: There are: 10 Protein residues -63: Analysing Protein... -63: -63: This run will generate roughly 0 Mb of data -63: Selected 2: 'Protein-H' -63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (285 ms) -63: [----------] 1 test from ConvertTprNoVelocityTest (285 ms total) -63: -63: [----------] Global test environment tear-down -63: [==========] 2 tests from 2 test suites ran. (590 ms total) -63: [ PASSED ] 2 tests. -63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 0.60 sec -test 64 - Start 64: FileIOTests - -64: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/FileIOTests.xml" -64: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/fileio/tests -64: Test timeout computed to be: 30 -64: [==========] Running 421 tests from 17 test suites. -64: [----------] Global test environment set-up. -64: [----------] 4 tests from Checkpoint -64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent -64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) -64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent -64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) -64: [ RUN ] Checkpoint.KvtRoundTripInt64 -64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) -64: [ RUN ] Checkpoint.KvtRoundTripReal -64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) -64: [----------] 4 tests from Checkpoint (0 ms total) -64: -64: [----------] 1 test from StructureIOTest -64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids -64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) -64: [----------] 1 test from StructureIOTest (0 ms total) -64: -64: [----------] 2 tests from FileMD5Test -64: [ RUN ] FileMD5Test.CanComputeMD5 -64: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) -64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong -64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) -64: [----------] 2 tests from FileMD5Test (1 ms total) -64: -64: [----------] 4 tests from FileTypeTest -64: [ RUN ] FileTypeTest.CorrectValueForEmptyString -64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForNoExtension -64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension -64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) -64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters -64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) -64: [----------] 4 tests from FileTypeTest (0 ms total) -64: -64: [----------] 4 tests from ColorMapTest -64: [ RUN ] ColorMapTest.CanReadFromFile -64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) -64: [ RUN ] ColorMapTest.CanWriteToFile -64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) -64: [ RUN ] ColorMapTest.RoundTrip -64: [ OK ] ColorMapTest.RoundTrip (0 ms) -64: [ RUN ] ColorMapTest.SearchWorks -64: [ OK ] ColorMapTest.SearchWorks (0 ms) -64: [----------] 4 tests from ColorMapTest (0 ms total) -64: -64: [----------] 4 tests from MatioTest -64: [ RUN ] MatioTest.CanWriteToFile -64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) -64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix -64: Converted a 4x3 matrix with 4 levels to reals -64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) -64: [ RUN ] MatioTest.CanConvertToNewRealMatrix -64: Converted a 4x3 matrix with 4 levels to reals -64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) -64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting -64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) -64: [----------] 4 tests from MatioTest (2 ms total) -64: -64: [----------] 3 tests from MrcSerializer -64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet -64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) -64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize -64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) -64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip -64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) -64: [----------] 3 tests from MrcSerializer (0 ms total) -64: -64: [----------] 4 tests from MrcDensityMap -64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent -64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) -64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent -64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) -64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile -64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) -64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile -64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) -64: [----------] 4 tests from MrcDensityMap (1 ms total) -64: -64: [----------] 8 tests from MrcDensityMapHeaderTest -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader -64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect -64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid -64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents -64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) -64: [ RUN ] MrcDensityMapHeaderTest.IsSane -64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) -64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) -64: -64: [----------] 10 tests from ReadTest -64: [ RUN ] ReadTest.get_eint_ReadsInteger -64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat -64: -64: ERROR 1 [file unknown]: -64: Right hand side '0.8' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) -64: [ RUN ] ReadTest.get_eint_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.get_eint64_ReadsInteger -64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat -64: -64: ERROR 1 [file unknown]: -64: Right hand side '0.8' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) -64: [ RUN ] ReadTest.get_eint64_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not an -64: integer value -64: -64: -64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.get_ereal_ReadsInteger -64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) -64: [ RUN ] ReadTest.get_ereal_ReadsFloat -64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) -64: [ RUN ] ReadTest.get_ereal_WarnsAboutString -64: -64: ERROR 1 [file unknown]: -64: Right hand side 'hello' for parameter 'test' in parameter file is not a -64: real value -64: -64: -64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) -64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString -64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) -64: [----------] 10 tests from ReadTest (0 ms total) -64: -64: [----------] 3 tests from TimeControlTest -64: [ RUN ] TimeControlTest.UnSetHasNoValue -64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) -64: [ RUN ] TimeControlTest.CanSetValue -64: [ OK ] TimeControlTest.CanSetValue (0 ms) -64: [ RUN ] TimeControlTest.CanUnsetValueAgain -64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) -64: [----------] 3 tests from TimeControlTest (0 ms total) -64: -64: [----------] 1 test from FileIOXdrSerializerTest -64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect -64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) -64: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) -64: -64: [----------] 1 test from TngTest -64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal -64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) -64: [----------] 1 test from TngTest (0 ms total) -64: -64: [----------] 4 tests from XvgioTest -64: [ RUN ] XvgioTest.readXvgIntWorks -64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgRealWorks -64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks -64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) -64: [ RUN ] XvgioTest.readXvgDeprecatedWorks -64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) -64: [----------] 4 tests from XvgioTest (0 ms total) -64: -64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (1 ms) -64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 -64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) -64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (2 ms total) -64: -64: [----------] 360 tests from FileTypeMatch/FileTypeTest -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) -64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 -64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) -64: [----------] 360 tests from FileTypeMatch/FileTypeTest (2 ms total) -64: -64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) -64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 -64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) -64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (1 ms total) -64: -64: [----------] Global test environment tear-down -64: [==========] 421 tests from 17 test suites ran. (14 ms total) -64: [ PASSED ] 421 tests. -64/92 Test #64: FileIOTests ............................... Passed 0.04 sec -test 65 - Start 65: SelectionUnitTests - -65: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" -65: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/selection/tests -65: Test timeout computed to be: 30 -65: [==========] Running 201 tests from 11 test suites. -65: [----------] Global test environment set-up. -65: [----------] 1 test from IndexGroupTest -65: [ RUN ] IndexGroupTest.RemovesDuplicates -65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) -65: [----------] 1 test from IndexGroupTest (0 ms total) -65: -65: [----------] 15 tests from IndexBlockTest -65: [ RUN ] IndexBlockTest.CreatesUnknownBlock -65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) -65: [ RUN ] IndexBlockTest.CreatesAtomBlock -65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) -65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology -65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology -65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology -65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology -65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) -65: [ RUN ] IndexBlockTest.CreatesSingleBlock -65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive -65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive -65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative -65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) -65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative -65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) -65: [----------] 15 tests from IndexBlockTest (1 ms total) -65: -65: [----------] 11 tests from IndexMapTest -65: [ RUN ] IndexMapTest.InitializesAtomBlock -65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom -65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (131 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle -65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue -65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule -65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) -65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll -65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) -65: [ RUN ] IndexMapTest.InitializesMoleculeBlock -65: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) -65: [ RUN ] IndexMapTest.MapsSingleBlock -65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) -65: [ RUN ] IndexMapTest.MapsResidueBlocks -65: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) -65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask -65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) -65: [ RUN ] IndexMapTest.HandlesMultipleRequests -65: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) -65: [----------] 11 tests from IndexMapTest (133 ms total) -65: -65: [----------] 3 tests from IndexGroupsAndNamesTest -65: [ RUN ] IndexGroupsAndNamesTest.containsNames -65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) -65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing -65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) -65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect -65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) -65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) -65: -65: [----------] 15 tests from NeighborhoodSearchTest -65: [ RUN ] NeighborhoodSearchTest.SimpleSearch -65: [ OK ] NeighborhoodSearchTest.SimpleSearch (9 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY -65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (10 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchBox -65: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic -65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (5 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC -65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC -65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox -65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch -65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch -65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (24 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches -65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC -65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC -65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) -65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs -65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) -65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions -65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) -65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions -65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) -65: [----------] 15 tests from NeighborhoodSearchTest (60 ms total) -65: -65: [----------] 13 tests from PositionCalculationTest -65: [ RUN ] PositionCalculationTest.ComputesAtomPositions -65: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex -65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions -65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions -65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions -65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions -65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole -65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax -65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) -65: [ RUN ] PositionCalculationTest.ComputesPositionMask -65: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms -65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 -65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations -65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) -65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations -65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) -65: [----------] 13 tests from PositionCalculationTest (3 ms total) -65: -65: [----------] 33 tests from SelectionCollectionTest -65: [ RUN ] SelectionCollectionTest.HandlesNoSelections -65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType -65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests -65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry -65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) -65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile -65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace -65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions -65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 -65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 -65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference -65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed -65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 -65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo -65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes -65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo -65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) -65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 -65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) -65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 -65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) -65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection -65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) -65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection -65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) -65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection -65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) -65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately -65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) -65: [----------] 33 tests from SelectionCollectionTest (10 ms total) -65: -65: [----------] 14 tests from SelectionCollectionInteractiveTest -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation -65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups -65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections -65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus -65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline -65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections -65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine -65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput -65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) -65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively -65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) -65: [----------] 14 tests from SelectionCollectionInteractiveTest (5 ms total) -65: -65: [----------] 70 tests from SelectionCollectionDataTest -65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone -65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr -65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResnr -65: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex -65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex -65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname -65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname -65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype -65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesChain -65: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMass -65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesCharge -65: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc -65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode -65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy -65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBeta -65: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesResname -65: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue -65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName -65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword -65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier -65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) -65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges -65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) -65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology -65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets -65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames -65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections -65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed -65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections -65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed -65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions -65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges -65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges -65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode -65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching -65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching -65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean -65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters -65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions -65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame -65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords -65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods -65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions -65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic -65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons -65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions -65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables -65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables -65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables -65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier -65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable -65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables -65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables -65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables -65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) -65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 -65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) -65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation -65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) -65: [----------] 70 tests from SelectionCollectionDataTest (41 ms total) -65: -65: [----------] 17 tests from SelectionOptionTest -65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection -65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired -65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired -65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired -65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksEmptySelections -65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) -65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections -65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooManySelections -65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections -65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText -65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesAdjuster -65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection -65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections -65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection -65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) -65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster -65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) -65: [----------] 17 tests from SelectionOptionTest (4 ms total) -65: -65: [----------] 9 tests from SelectionFileOptionTest -65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile -65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions -65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile -65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile -65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet -65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) -65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile -65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile -65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile -65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) -65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles -65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) -65: [----------] 9 tests from SelectionFileOptionTest (2 ms total) -65: -65: [----------] Global test environment tear-down -65: [==========] 201 tests from 11 test suites ran. (263 ms total) -65: [ PASSED ] 201 tests. -65/92 Test #65: SelectionUnitTests ........................ Passed 0.28 sec -test 66 - Start 66: MdrunOutputTests - -66: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" -66: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -66: Test timeout computed to be: 600 -66: [==========] Running 12 tests from 5 test suites. -66: [----------] Global test environment set-up. -66: [----------] 1 test from MdrunTest -66: [ RUN ] MdrunTest.WritesHelp -66: [ OK ] MdrunTest.WritesHelp (33 ms) -66: [----------] 1 test from MdrunTest (33 ms total) -66: -66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -138432513 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.098 0.049 199.7 -66: (ns/day) (hour/ns) -66: Performance: 3.529 6.800 -66: Reading frame 0 time 0.000 -66: # Atoms 6 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (59 ms) -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -478365834 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.090 0.045 199.7 -66: (ns/day) (hour/ns) -66: Performance: 3.838 6.253 -66: Reading frame 0 time 0.000 -66: # Atoms 6 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (51 ms) -66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 -66: Generating 1-4 interactions: fudge = 0.5 -66: Number of degrees of freedom in T-Coupling group rest is 9.00 -66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -66: NVE simulation: will use the initial temperature of 2573.591 K for -66: determining the Verlet buffer size -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There were 2 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc2' -66: 1 steps, 0.0 ps. -66: Setting the LD random seed to -1357972225 -66: -66: Generated 3 of the 3 non-bonded parameter combinations -66: -66: Generated 3 of the 3 1-4 parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.049 0.024 199.7 -66: (ns/day) (hour/ns) -66: Performance: 7.074 3.393 -66: Reading frame 0 time 0.000 -66: # Atoms 3 -66: Reading frame 1 time 0.001 Last frame 1 time 0.001 -66: -66: -66: Item #frames Timestep (ps) -66: Step 2 0.001 -66: Time 2 0.001 -66: Lambda 0 -66: Coords 2 0.001 -66: Velocities 0 -66: Forces 0 -66: Box 2 0.001 -66: Checking file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc -66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (34 ms) -66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (144 ms total) -66: -66: [----------] 2 tests from Argon12/OutputFiles -66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -66: that with the Verlet scheme, nstlist has no effect on the accuracy of -66: your simulation. -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: Setting nstcalcenergy (100) equal to nstenergy (4) -66: -66: Number of degrees of freedom in T-Coupling group System is 33.00 -66: -66: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -66: NVE simulation: will use the initial temperature of 68.810 K for -66: determining the Verlet buffer size -66: -66: -66: There were 3 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'Argon' -66: 16 steps, 0.0 ps. -66: Generated 1 of the 1 non-bonded parameter combinations -66: -66: Excluding 1 bonded neighbours molecule type 'Argon' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -66: -66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -66: -66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.056 0.028 199.7 -66: (ns/day) (hour/ns) -66: Performance: 51.990 0.462 -66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (32 ms) -66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -66: that with the Verlet scheme, nstlist has no effect on the accuracy of -66: your simulation. -66: -66: -66: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: Setting nstcalcenergy (100) equal to nstenergy (4) -66: -66: Number of degrees of freedom in T-Coupling group System is 33.00 -66: -66: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -66: NVE simulation: will use the initial temperature of 68.810 K for -66: determining the Verlet buffer size -66: -66: -66: There were 3 NOTEs -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Can not increase nstlist because an NVE ensemble is used -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'Argon' -66: 16 steps, 0.0 ps. -66: Generated 1 of the 1 non-bonded parameter combinations -66: -66: Excluding 1 bonded neighbours molecule type 'Argon' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -66: -66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -66: -66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.119 0.059 199.8 -66: (ns/day) (hour/ns) -66: Performance: 24.753 0.970 -66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (64 ms) -66: [----------] 2 tests from Argon12/OutputFiles (97 ms total) -66: -66: [----------] 3 tests from MdrunCanWrite/Trajectories -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to -271069441 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.030 0.015 199.4 -66: (ns/day) (hour/ns) -66: Performance: 40.252 0.596 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (20 ms) -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to 1664544639 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.051 0.026 199.6 -66: (ns/day) (hour/ns) -66: Performance: 23.528 1.020 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (34 ms) -66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 6 steps, 0.0 ps. -66: Setting the LD random seed to -874341765 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.056 0.028 199.6 -66: (ns/day) (hour/ns) -66: Performance: 21.431 1.120 -66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (34 ms) -66: [----------] 3 tests from MdrunCanWrite/Trajectories (89 ms total) -66: -66: [----------] 3 tests from MdrunCanWrite/NptTrajectories -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to 1991507439 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.045 0.022 199.6 -66: (ns/day) (hour/ns) -66: Performance: 11.623 2.065 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (27 ms) -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 -66: -66: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -66: The Berendsen barostat does not generate any strictly correct ensemble, -66: and should not be used for new production simulations (in our opinion). -66: We recommend using the C-rescale barostat instead. -66: -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: -66: There was 1 WARNING -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to -805519521 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.012 0.006 198.6 -66: (ns/day) (hour/ns) -66: Performance: 41.514 0.578 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (11 ms) -66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 -66: Number of degrees of freedom in T-Coupling group System is 12.00 -66: -66: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: -66: You are using a plain Coulomb cut-off, which might produce artifacts. -66: You might want to consider using PME electrostatics. -66: -66: -66: -66: There was 1 NOTE -66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -66: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 -66: -66: Using 1 MPI thread -66: Using 2 OpenMP threads -66: -66: -66: NOTE: The number of threads is not equal to the number of (logical) cpus -66: and the -pin option is set to auto: will not pin threads to cpus. -66: This can lead to significant performance degradation. -66: Consider using -pin on (and -pinoffset in case you run multiple jobs). -66: starting mdrun 'spc-and-methanol' -66: 2 steps, 0.0 ps. -66: Setting the LD random seed to -16990274 -66: -66: Generated 8 of the 10 non-bonded parameter combinations -66: -66: Excluding 2 bonded neighbours molecule type 'Methanol' -66: -66: Excluding 2 bonded neighbours molecule type 'SOL' -66: -66: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -66: -66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -66: -66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -66: -66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -66: -66: Note that mdrun will redetermine rlist based on the actual pair-list setup -66: -66: This run will generate roughly 0 Mb of data -66: -66: Writing final coordinates. -66: -66: Core t (s) Wall t (s) (%) -66: Time: 0.022 0.011 199.2 -66: (ns/day) (hour/ns) -66: Performance: 23.315 1.029 -66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (18 ms) -66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (58 ms total) -66: -66: [----------] Global test environment tear-down -66: [==========] 12 tests from 5 test suites ran. (558 ms total) -66: [ PASSED ] 12 tests. -66/92 Test #66: MdrunOutputTests .......................... Passed 0.57 sec -test 67 - Start 67: MdrunModulesTests - -67: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" -67: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -67: Test timeout computed to be: 600 -67: [==========] Running 15 tests from 3 test suites. -67: [----------] Global test environment set-up. -67: [----------] 9 tests from DensityFittingTest -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -3.85652562592421e+03 -67: Maximum force = 4.50998690851897e+03 on atom 3 -67: Norm of force = 1.68168494163492e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2112815068 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (8 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -9.82077921283928e+03 -67: Maximum force = 7.39548334240075e+03 on atom 2 -67: Norm of force = 2.78250777177324e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1210100738 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (23 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (5 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Overriding nsteps with value passed on the command line: 4 steps -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 4 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 5 steps. -67: Potential Energy = -5.47393359520241e+03 -67: Maximum force = 6.13219949575544e+03 on atom 2 -67: Norm of force = 1.77021426574818e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -171250209 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (6 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (8 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -3.85652562592421e+03 -67: Maximum force = 4.50998690851897e+03 on atom 3 -67: Norm of force = 1.68168494163492e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -6316289 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (16 ms) -67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = -2.71386626041483e+04 -67: Maximum force = 6.78276504921089e+03 on atom 2 -67: Norm of force = 1.96088640980697e+03 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -186318883 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (4 ms) -67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch -67: -67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. -67: Setting the LD random seed to 1861156593 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (12 ms) -67: [ RUN ] DensityFittingTest.CheckpointWorks -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -67: Setting nstcalcenergy (100) equal to nstenergy (2) -67: -67: Number of degrees of freedom in T-Coupling group rest is 33.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -67: NVE simulation: will use the initial temperature of 68.810 K for -67: determining the Verlet buffer size -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting mdrun 'Argon' -67: 2 steps, 0.0 ps. -67: Setting the LD random seed to -288366593 -67: -67: Generated 1 of the 1 non-bonded parameter combinations -67: -67: Excluding 1 bonded neighbours molecule type 'Argon' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.023 0.011 198.9 -67: (ns/day) (hour/ns) -67: Performance: 22.688 1.058 -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps -67: Can not increase nstlist because an NVE ensemble is used -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting mdrun 'Argon' -67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.015 0.008 198.4 -67: (ns/day) (hour/ns) -67: Performance: 56.612 0.424 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (28 ms) -67: [----------] 9 tests from DensityFittingTest (114 ms total) -67: -67: [----------] 4 tests from MimicTest -67: [ RUN ] MimicTest.OneQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 31 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.000 0.000 188.0 -67: (ns/day) (hour/ns) -67: Performance: 325.303 0.074 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -50356259 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.OneQuantumMol (8 ms) -67: [ RUN ] MimicTest.AllQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 29 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.000 0.000 186.9 -67: (ns/day) (hour/ns) -67: Performance: 377.881 0.064 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1120538637 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.AllQuantumMol (6 ms) -67: [ RUN ] MimicTest.TwoQuantumMol -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 21.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: NVE simulation with an initial temperature of zero: will use a Verlet -67: buffer of 10%. Check your energy drift! -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -67: -67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 38 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.001 0.000 187.8 -67: (ns/day) (hour/ns) -67: Performance: 273.914 0.088 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -68157953 -67: -67: Generated 10 of the 10 non-bonded parameter combinations -67: -67: Generated 10 of the 10 1-4 parameter combinations -67: -67: Excluding 2 bonded neighbours molecule type 'SOL' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.TwoQuantumMol (5 ms) -67: [ RUN ] MimicTest.BondCuts -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: For a correct single-point energy evaluation with nsteps = 0, use -67: continuation = yes to avoid constraining the input coordinates. -67: -67: Generating 1-4 interactions: fudge = 0.5 -67: Number of degrees of freedom in T-Coupling group rest is 66.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: NVE simulation: will use the initial temperature of 300.368 K for -67: determining the Verlet buffer size -67: -67: -67: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 3 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Can not increase nstlist because an NVE ensemble is used -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -67: -67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -67: Reading frame 0 time 0.000 Last frame 0 time 0.000 -67: -67: NOTE: 20 % of the run time was spent in pair search, -67: you might want to increase nstlist (this has no effect on accuracy) -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.001 0.000 192.0 -67: (ns/day) (hour/ns) -67: Performance: 213.672 0.112 -67: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file -67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1943010288 -67: -67: Generated 2211 of the 2211 non-bonded parameter combinations -67: -67: Generated 2211 of the 2211 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] MimicTest.BondCuts (15 ms) -67: [----------] 4 tests from MimicTest (36 ms total) -67: -67: [----------] 2 tests from WithIntegrator/ImdTest -67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 -67: Generating 1-4 interactions: fudge = 1 -67: -67: NOTE 1 [file glycine_vacuo.top, line 12]: -67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an -67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times -67: the time step of 2.0e-03 ps. -67: Maybe you forgot to change the constraints mdp option. -67: -67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -67: Number of degrees of freedom in T-Coupling group System is 27.00 -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 -67: -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: IMD: Enabled. This simulation will accept incoming IMD connections. -67: IMD: Pulling from IMD remote is enabled (-imdpull). -67: IMD: Setting port for connection requests to 0. -67: IMD: Setting up incoming socket. -67: IMD: Listening for IMD connection on port 48967. -67: IMD: -imdwait not set, starting simulation. -67: starting mdrun 'Glycine' -67: 2 steps, 0.0 ps. -67: Setting the LD random seed to -539100981 -67: -67: Generated 20503 of the 20503 non-bonded parameter combinations -67: -67: Generated 17396 of the 20503 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Glycine' -67: -67: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero -67: -67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -67: -67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -67: -67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm -67: -67: Note that mdrun will redetermine rlist based on the actual pair-list setup -67: -67: This run will generate roughly 0 Mb of data -67: -67: Writing final coordinates. -67: -67: Core t (s) Wall t (s) (%) -67: Time: 0.409 0.205 199.9 -67: (ns/day) (hour/ns) -67: Performance: 2.534 9.473 -67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (353 ms) -67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 -67: -67: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not -67: apply to steep. -67: -67: Generating 1-4 interactions: fudge = 1 -67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -67: Number of degrees of freedom in T-Coupling group System is 27.00 -67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -67: -67: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -67: You are using a plain Coulomb cut-off, which might produce artifacts. -67: You might want to consider using PME electrostatics. -67: -67: -67: -67: There were 2 NOTEs -67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -67: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -67: Using 1 MPI thread -67: Using 2 OpenMP threads -67: -67: -67: NOTE: The number of threads is not equal to the number of (logical) cpus -67: and the -pin option is set to auto: will not pin threads to cpus. -67: This can lead to significant performance degradation. -67: Consider using -pin on (and -pinoffset in case you run multiple jobs). -67: -67: IMD: Enabled. This simulation will accept incoming IMD connections. -67: IMD: Pulling from IMD remote is enabled (-imdpull). -67: IMD: Setting port for connection requests to 0. -67: IMD: Setting up incoming socket. -67: IMD: Listening for IMD connection on port 48033. -67: IMD: -imdwait not set, starting simulation. -67: -67: Steepest Descents: -67: Tolerance (Fmax) = 1.00000e+01 -67: Number of steps = 2 -67: -67: Energy minimization reached the maximum number of steps before the forces -67: reached the requested precision Fmax < 10. -67: -67: writing lowest energy coordinates. -67: -67: Steepest Descents did not converge to Fmax < 10 in 3 steps. -67: Potential Energy = 1.19770464690297e+03 -67: Maximum force = 1.77948604657897e+04 on atom 9 -67: Norm of force = 7.87328617833981e+03 -67: Setting the LD random seed to -84845649 -67: -67: Generated 20503 of the 20503 non-bonded parameter combinations -67: -67: Generated 17396 of the 20503 1-4 parameter combinations -67: -67: Excluding 3 bonded neighbours molecule type 'Glycine' -67: -67: This run will generate roughly 0 Mb of data -67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (65 ms) -67: [----------] 2 tests from WithIntegrator/ImdTest (419 ms total) -67: -67: [----------] Global test environment tear-down -67: [==========] 15 tests from 3 test suites ran. (681 ms total) -67: [ PASSED ] 15 tests. -67/92 Test #67: MdrunModulesTests ......................... Passed 0.69 sec -test 68 - Start 68: MdrunIOTests - -68: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" -68: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -68: Test timeout computed to be: 600 -68: [==========] Running 76 tests from 13 test suites. -68: [----------] Global test environment set-up. -68: [----------] 9 tests from GromppTest -68: [ RUN ] GromppTest.EmptyMdpFileWorks -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -4497825 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.EmptyMdpFileWorks (47 ms) -68: [ RUN ] GromppTest.SimulatedAnnealingWorks -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Simulated annealing for group rest: Periodic, 4 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 2.0 320.0 -68: 4.0 320.0 -68: 6.0 298.0 -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to 1006630909 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) -68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Simulated annealing for group Methanol: Single, 3 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 3.0 280.0 -68: 6.0- 270.0 -68: Simulated annealing for group SOL: Periodic, 4 timepoints -68: Time (ps) Temperature (K) -68: 0.0 298.0 -68: 2.0 320.0 -68: 4.0 320.0 -68: 6.0 298.0 -68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 -68: Number of degrees of freedom in T-Coupling group SOL is 4.80 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -141566001 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) -68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError -68: Setting the LD random seed to 2147331068 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (6 ms) -68: [ RUN ] GromppTest.HandlesMaxwarn -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: -68: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: The Berendsen thermostat does not generate the correct kinetic energy -68: distribution, and should not be used for new production simulations (in -68: our opinion). We would recommend the V-rescale thermostat. -68: -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: -68: There was 1 WARNING -68: Setting the LD random seed to -209753154 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.HandlesMaxwarn (4 ms) -68: [ RUN ] GromppTest.MaxwarnShouldBePositive -68: [ OK ] GromppTest.MaxwarnShouldBePositive (1 ms) -68: [ RUN ] GromppTest.ValidTransformationCoord -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Pull group 1 'SOL' has 3 atoms -68: Pull group 2 'Methanol' has 3 atoms -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: -68: There were 3 NOTEs -68: Setting the LD random seed to -1651507457 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: [ OK ] GromppTest.ValidTransformationCoord (4 ms) -68: [ RUN ] GromppTest.InvalidTransformationCoord -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: For a correct single-point energy evaluation with nsteps = 0, use -68: continuation = yes to avoid constraining the input coordinates. -68: -68: Pull group 1 'SOL' has 3 atoms -68: Pull group 2 'Methanol' has 3 atoms -68: Number of degrees of freedom in T-Coupling group rest is 12.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: NVE simulation: will use the initial temperature of 1046.791 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 5 -68: 2 3 2 0.613 nm 0.000 nm -68: 1 3 5 -68: 2 3 2 Setting the LD random seed to -75530371 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) -68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic -68: Setting the LD random seed to -852014 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (6 ms) -68: [----------] 9 tests from GromppTest (80 ms total) -68: -68: [----------] 6 tests from MdrunTerminationTest -68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to 2113304570 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.562 0.281 199.9 -68: (ns/day) (hour/ns) -68: Performance: 0.922 26.031 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.011 0.006 198.5 -68: (ns/day) (hour/ns) -68: Performance: 46.585 0.515 -68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (298 ms) -68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 1, rlist from 1.035 to 1 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 100 steps, 0.1 ps. -68: -68: Step 5: Run time exceeded 0.000 hours, will terminate the run within 200 steps -68: Setting the LD random seed to -75966561 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.289 0.145 199.9 -68: (ns/day) (hour/ns) -68: Performance: 60.281 0.398 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 102 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 100 -68: Runtime for the run 0.1 ps -68: Run end step 100 -68: Run end time 0.1 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 102 -68: Runtime for the run 0.102 ps -68: Run end step 102 -68: Run end time 0.102 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.007 0.003 198.1 -68: (ns/day) (hour/ns) -68: Performance: 76.308 0.315 -68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (199 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to 1876948663 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.064 0.032 199.6 -68: (ns/day) (hour/ns) -68: Performance: 8.120 2.956 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.207 0.104 199.9 -68: (ns/day) (hour/ns) -68: Performance: 2.504 9.586 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 6 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 6 -68: Runtime for the run 0.006 ps -68: Run end step 6 -68: Run end time 0.006 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.008 199.5 -68: (ns/day) (hour/ns) -68: Performance: 31.209 0.769 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 8 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 6 -68: Runtime for the run 0.006 ps -68: Run end step 6 -68: Run end time 0.006 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 8 -68: Runtime for the run 0.008 ps -68: Run end step 8 -68: Run end time 0.008 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.389 0.195 200.0 -68: (ns/day) (hour/ns) -68: Performance: 1.331 18.034 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: NOTE: 27 % of the run time was spent in pair search, -68: you might want to increase nstlist (this has no effect on accuracy) -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.000 0.000 177.9 -68: (ns/day) (hour/ns) -68: Performance: 564.467 0.043 -68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (416 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to 396343379 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 18.007 1.333 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps. -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.487 0.743 200.0 -68: (ns/day) (hour/ns) -68: Performance: 0.581 41.301 -68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (802 ms) -68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -597721603 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.048 0.024 199.6 -68: (ns/day) (hour/ns) -68: Performance: 10.842 2.214 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 4 -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (53 ms) -68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to 2142753679 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 198.5 -68: (ns/day) (hour/ns) -68: Performance: 37.275 0.644 -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Setting nsteps to 4 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -68: Input file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 2 -68: Runtime for the run 0.002 ps -68: Run end step 2 -68: Run end time 0.002 ps -68: -68: -68: Output file: -68: Run start step 0 -68: Run start time 0 ps -68: Step to be made during run 4 -68: Runtime for the run 0.004 ps -68: Run end step 4 -68: Run end time 0.004 ps -68: -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 199.5 -68: (ns/day) (hour/ns) -68: Performance: 20.551 1.168 -68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (39 ms) -68: [----------] 6 tests from MdrunTerminationTest (1809 ms total) -68: -68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks -68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.028 0.014 199.4 -68: (ns/day) (hour/ns) -68: Performance: 106.005 0.226 -68: trr version: GMX_trn_file (double precision) -68: -68: -68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (21 ms) -68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.013 199.5 -68: (ns/day) (hour/ns) -68: Performance: 110.113 0.218 -68: -68: -68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (30 ms) -68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (52 ms total) -68: -68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.062 0.031 199.7 -68: (ns/day) (hour/ns) -68: Performance: 47.228 0.508 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.051 0.025 199.6 -68: (ns/day) (hour/ns) -68: Performance: 30.625 0.784 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.281 0.141 199.9 -68: (ns/day) (hour/ns) -68: Performance: 5.522 4.346 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (225 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.919 0.960 200.0 -68: (ns/day) (hour/ns) -68: Performance: 1.531 15.679 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.112 0.056 199.8 -68: (ns/day) (hour/ns) -68: Performance: 13.866 1.731 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.061 0.031 199.6 -68: (ns/day) (hour/ns) -68: Performance: 25.342 0.947 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1068 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.087 0.044 199.7 -68: (ns/day) (hour/ns) -68: Performance: 33.612 0.714 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.042 0.021 199.6 -68: (ns/day) (hour/ns) -68: Performance: 37.274 0.644 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.020 199.3 -68: (ns/day) (hour/ns) -68: Performance: 39.400 0.609 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (105 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.019 199.6 -68: (ns/day) (hour/ns) -68: Performance: 75.769 0.317 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.075 0.037 199.8 -68: (ns/day) (hour/ns) -68: Performance: 20.784 1.155 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 199.0 -68: (ns/day) (hour/ns) -68: Performance: 53.090 0.452 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (91 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.010 199.3 -68: (ns/day) (hour/ns) -68: Performance: 140.052 0.171 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.1 -68: (ns/day) (hour/ns) -68: Performance: 81.041 0.296 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.3 -68: (ns/day) (hour/ns) -68: Performance: 59.847 0.401 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (48 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.061 0.031 199.7 -68: (ns/day) (hour/ns) -68: Performance: 47.755 0.503 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 71.208 0.337 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.4 -68: (ns/day) (hour/ns) -68: Performance: 48.403 0.496 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (72 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 196.8 -68: (ns/day) (hour/ns) -68: Performance: 134.174 0.179 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.272 0.136 199.9 -68: (ns/day) (hour/ns) -68: Performance: 5.724 4.193 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.5 -68: (ns/day) (hour/ns) -68: Performance: 58.794 0.408 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (179 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 199.5 -68: (ns/day) (hour/ns) -68: Performance: 114.945 0.209 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.066 0.033 199.6 -68: (ns/day) (hour/ns) -68: Performance: 23.598 1.017 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.117 0.058 199.8 -68: (ns/day) (hour/ns) -68: Performance: 13.293 1.805 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (137 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 133.499 0.180 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.2 -68: (ns/day) (hour/ns) -68: Performance: 86.855 0.276 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.008 199.2 -68: (ns/day) (hour/ns) -68: Performance: 92.036 0.261 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (42 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.5 -68: (ns/day) (hour/ns) -68: Performance: 98.891 0.243 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.043 0.021 199.6 -68: (ns/day) (hour/ns) -68: Performance: 36.395 0.659 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.697 0.849 200.0 -68: (ns/day) (hour/ns) -68: Performance: 0.916 26.192 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (909 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.360 0.180 199.9 -68: (ns/day) (hour/ns) -68: Performance: 8.154 2.943 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.008 199.4 -68: (ns/day) (hour/ns) -68: Performance: 92.997 0.258 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.3 -68: (ns/day) (hour/ns) -68: Performance: 70.990 0.338 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (488 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.084 0.042 199.8 -68: (ns/day) (hour/ns) -68: Performance: 34.859 0.688 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.060 0.030 199.7 -68: (ns/day) (hour/ns) -68: Performance: 25.946 0.925 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.078 0.039 199.6 -68: (ns/day) (hour/ns) -68: Performance: 19.845 1.209 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (129 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 197.9 -68: (ns/day) (hour/ns) -68: Performance: 120.567 0.199 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.075 0.037 199.7 -68: (ns/day) (hour/ns) -68: Performance: 20.829 1.152 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.073 0.036 199.7 -68: (ns/day) (hour/ns) -68: Performance: 21.356 1.124 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (110 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.059 0.030 199.3 -68: (ns/day) (hour/ns) -68: Performance: 49.563 0.484 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.104 0.052 199.8 -68: (ns/day) (hour/ns) -68: Performance: 14.974 1.603 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.068 0.034 199.3 -68: (ns/day) (hour/ns) -68: Performance: 22.747 1.055 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (143 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.084 0.042 199.8 -68: (ns/day) (hour/ns) -68: Performance: 34.877 0.688 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.117 0.059 199.8 -68: (ns/day) (hour/ns) -68: Performance: 13.228 1.814 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.052 0.026 199.5 -68: (ns/day) (hour/ns) -68: Performance: 29.772 0.806 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (156 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.016 199.2 -68: (ns/day) (hour/ns) -68: Performance: 93.673 0.256 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.2 -68: (ns/day) (hour/ns) -68: Performance: 78.812 0.305 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.052 0.026 199.6 -68: (ns/day) (hour/ns) -68: Performance: 29.601 0.811 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (151 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.240 0.620 200.0 -68: (ns/day) (hour/ns) -68: Performance: 2.369 10.129 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.062 0.031 199.4 -68: (ns/day) (hour/ns) -68: Performance: 25.163 0.954 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.046 0.023 199.1 -68: (ns/day) (hour/ns) -68: Performance: 33.392 0.719 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (1036 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.1 -68: (ns/day) (hour/ns) -68: Performance: 91.710 0.262 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.078 0.039 199.6 -68: (ns/day) (hour/ns) -68: Performance: 19.844 1.209 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.120 0.060 199.7 -68: (ns/day) (hour/ns) -68: Performance: 12.972 1.850 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (249 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.130 0.065 199.7 -68: (ns/day) (hour/ns) -68: Performance: 22.644 1.060 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.014 199.3 -68: (ns/day) (hour/ns) -68: Performance: 54.379 0.441 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.033 0.016 199.4 -68: (ns/day) (hour/ns) -68: Performance: 47.583 0.504 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (224 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: NVE simulation: will use the initial temperature of 456.887 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 6 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.051 0.026 199.3 -68: (ns/day) (hour/ns) -68: Performance: 57.452 0.418 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 2.359 1.180 200.0 -68: (ns/day) (hour/ns) -68: Performance: 0.659 36.405 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.147 0.074 199.8 -68: (ns/day) (hour/ns) -68: Performance: 10.559 2.273 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (1328 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.329 0.164 199.9 -68: (ns/day) (hour/ns) -68: Performance: 8.935 2.686 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.9 -68: (ns/day) (hour/ns) -68: Performance: 79.529 0.302 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.050 0.025 199.5 -68: (ns/day) (hour/ns) -68: Performance: 30.895 0.777 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (345 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 3.100 1.550 200.0 -68: (ns/day) (hour/ns) -68: Performance: 0.948 25.324 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.227 0.113 199.8 -68: (ns/day) (hour/ns) -68: Performance: 6.856 3.501 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.3 -68: (ns/day) (hour/ns) -68: Performance: 59.604 0.403 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (1819 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 129.754 0.185 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 198.8 -68: (ns/day) (hour/ns) -68: Performance: 89.572 0.268 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.010 199.0 -68: (ns/day) (hour/ns) -68: Performance: 75.132 0.319 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (82 ms) -68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: -68: NOTE 3 [file unknown]: -68: You are using constraints on all bonds, whereas the forcefield has been -68: parametrized only with constraints involving hydrogen atoms. We suggest -68: using constraints = h-bonds instead, this will also improve performance. -68: -68: Number of degrees of freedom in T-Coupling group System is 23.00 -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: There are 9 non-linear virtual site constructions. Their contribution to -68: the energy error is approximated. In most cases this does not affect the -68: error significantly. -68: -68: -68: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 5 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -68: -68: turning all bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -68: -68: Cleaning up constraints and constant bonded interactions with virtual sites -68: -68: Removed 18 Angles with virtual sites, 21 left -68: -68: Removed 10 Proper Dih.s with virtual sites, 44 left -68: -68: Converted 15 Constraints with virtual sites to connections, 7 left -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.393 0.196 199.9 -68: (ns/day) (hour/ns) -68: Performance: 7.481 3.208 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.014 199.0 -68: (ns/day) (hour/ns) -68: Performance: 53.745 0.447 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 -68: -68: Update groups can not be used for this system because an incompatible virtual site type is used -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine dipeptide in vacuo' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.083 0.041 199.7 -68: (ns/day) (hour/ns) -68: Performance: 18.754 1.280 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (334 ms) -68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (9482 ms total) -68: -68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 198.8 -68: (ns/day) (hour/ns) -68: Performance: 121.014 0.198 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.023 0.012 198.3 -68: (ns/day) (hour/ns) -68: Performance: 67.074 0.358 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.028 0.014 198.9 -68: (ns/day) (hour/ns) -68: Performance: 55.883 0.429 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (78 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.2 -68: (ns/day) (hour/ns) -68: Performance: 115.473 0.208 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.033 0.017 198.8 -68: (ns/day) (hour/ns) -68: Performance: 46.351 0.518 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.033 0.017 198.7 -68: (ns/day) (hour/ns) -68: Performance: 46.762 0.513 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.043 0.022 199.6 -68: (ns/day) (hour/ns) -68: Performance: 68.086 0.352 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.016 199.5 -68: (ns/day) (hour/ns) -68: Performance: 49.732 0.483 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 198.9 -68: (ns/day) (hour/ns) -68: Performance: 44.270 0.542 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (87 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: NVE simulation: will use the initial temperature of 294.908 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 4 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.037 0.018 199.5 -68: (ns/day) (hour/ns) -68: Performance: 79.861 0.301 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.475 0.238 199.9 -68: (ns/day) (hour/ns) -68: Performance: 3.274 7.330 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.100 0.050 199.6 -68: (ns/day) (hour/ns) -68: Performance: 15.443 1.554 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (340 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.064 0.032 199.4 -68: (ns/day) (hour/ns) -68: Performance: 45.571 0.527 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 199.0 -68: (ns/day) (hour/ns) -68: Performance: 43.606 0.550 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.041 0.021 199.4 -68: (ns/day) (hour/ns) -68: Performance: 37.656 0.637 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (124 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.048 0.024 199.1 -68: (ns/day) (hour/ns) -68: Performance: 61.485 0.390 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.043 0.022 199.0 -68: (ns/day) (hour/ns) -68: Performance: 36.006 0.667 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.1 -68: (ns/day) (hour/ns) -68: Performance: 58.454 0.411 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (216 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.127 0.064 199.7 -68: (ns/day) (hour/ns) -68: Performance: 23.068 1.040 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 198.2 -68: (ns/day) (hour/ns) -68: Performance: 44.356 0.541 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.092 0.046 199.6 -68: (ns/day) (hour/ns) -68: Performance: 16.777 1.431 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (176 ms) -68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.036 0.018 199.2 -68: (ns/day) (hour/ns) -68: Performance: 80.707 0.297 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.4 -68: (ns/day) (hour/ns) -68: Performance: 61.664 0.389 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 198.9 -68: (ns/day) (hour/ns) -68: Performance: 59.187 0.405 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (100 ms) -68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1202 ms total) -68: -68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.110 0.055 199.7 -68: (ns/day) (hour/ns) -68: Performance: 26.568 0.903 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.063 0.032 199.6 -68: (ns/day) (hour/ns) -68: Performance: 24.484 0.980 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.020 199.3 -68: (ns/day) (hour/ns) -68: Performance: 39.417 0.609 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (203 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.123 0.061 199.8 -68: (ns/day) (hour/ns) -68: Performance: 23.924 1.003 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 199.1 -68: (ns/day) (hour/ns) -68: Performance: 90.346 0.266 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.077 0.039 199.6 -68: (ns/day) (hour/ns) -68: Performance: 20.111 1.193 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (134 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.307 0.154 199.9 -68: (ns/day) (hour/ns) -68: Performance: 9.556 2.512 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.853 0.427 200.0 -68: (ns/day) (hour/ns) -68: Performance: 1.823 13.168 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.3 -68: (ns/day) (hour/ns) -68: Performance: 48.443 0.495 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (620 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.057 0.028 199.2 -68: (ns/day) (hour/ns) -68: Performance: 51.573 0.465 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 198.3 -68: (ns/day) (hour/ns) -68: Performance: 75.555 0.318 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 198.8 -68: (ns/day) (hour/ns) -68: Performance: 87.830 0.273 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (68 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.231 0.116 199.9 -68: (ns/day) (hour/ns) -68: Performance: 12.694 1.891 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.051 0.025 199.7 -68: (ns/day) (hour/ns) -68: Performance: 30.623 0.784 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.020 199.5 -68: (ns/day) (hour/ns) -68: Performance: 39.284 0.611 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (181 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.077 0.039 199.7 -68: (ns/day) (hour/ns) -68: Performance: 38.010 0.631 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.083 0.041 199.8 -68: (ns/day) (hour/ns) -68: Performance: 18.817 1.275 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 1.211 0.606 200.0 -68: (ns/day) (hour/ns) -68: Performance: 1.284 18.689 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (715 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.177 0.088 199.9 -68: (ns/day) (hour/ns) -68: Performance: 16.600 1.446 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.066 0.033 199.6 -68: (ns/day) (hour/ns) -68: Performance: 23.641 1.015 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.028 0.014 199.1 -68: (ns/day) (hour/ns) -68: Performance: 54.632 0.439 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (174 ms) -68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.3 -68: (ns/day) (hour/ns) -68: Performance: 98.856 0.243 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.3 -68: (ns/day) (hour/ns) -68: Performance: 48.671 0.493 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 -68: -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 198.5 -68: (ns/day) (hour/ns) -68: Performance: 51.883 0.463 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (66 ms) -68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (2164 ms total) -68: -68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact -68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.010 198.4 -68: (ns/day) (hour/ns) -68: Performance: 149.620 0.160 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.016 0.008 198.8 -68: (ns/day) (hour/ns) -68: Performance: 98.600 0.243 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 199.1 -68: (ns/day) (hour/ns) -68: Performance: 90.401 0.265 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (42 ms) -68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.6 -68: (ns/day) (hour/ns) -68: Performance: 111.445 0.215 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 199.4 -68: (ns/day) (hour/ns) -68: Performance: 46.178 0.520 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.057 0.029 199.3 -68: (ns/day) (hour/ns) -68: Performance: 27.181 0.883 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (74 ms) -68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (116 ms total) -68: -68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.036 0.018 199.1 -68: (ns/day) (hour/ns) -68: Performance: 82.299 0.292 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.026 0.013 199.1 -68: (ns/day) (hour/ns) -68: Performance: 59.261 0.405 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 198.9 -68: (ns/day) (hour/ns) -68: Performance: 70.379 0.341 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (209 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.094 0.047 199.7 -68: (ns/day) (hour/ns) -68: Performance: 31.237 0.768 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.025 0.013 198.7 -68: (ns/day) (hour/ns) -68: Performance: 60.750 0.395 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.020 0.010 199.1 -68: (ns/day) (hour/ns) -68: Performance: 78.620 0.305 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (88 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.019 0.009 199.0 -68: (ns/day) (hour/ns) -68: Performance: 156.380 0.153 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.024 0.012 199.2 -68: (ns/day) (hour/ns) -68: Performance: 65.596 0.366 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.039 0.020 199.4 -68: (ns/day) (hour/ns) -68: Performance: 39.282 0.611 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (57 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -68: 1 -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 138.297 0.174 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.010 199.2 -68: (ns/day) (hour/ns) -68: Performance: 74.601 0.322 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.013 199.3 -68: (ns/day) (hour/ns) -68: Performance: 58.129 0.413 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (50 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.029 0.015 199.4 -68: (ns/day) (hour/ns) -68: Performance: 100.398 0.239 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.5 -68: (ns/day) (hour/ns) -68: Performance: 52.344 0.459 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.013 198.9 -68: (ns/day) (hour/ns) -68: Performance: 57.834 0.415 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (63 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.027 0.013 199.4 -68: (ns/day) (hour/ns) -68: Performance: 109.549 0.219 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.038 0.019 199.6 -68: (ns/day) (hour/ns) -68: Performance: 41.059 0.585 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.045 0.023 199.4 -68: (ns/day) (hour/ns) -68: Performance: 34.478 0.696 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (69 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) -68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.6 -68: (ns/day) (hour/ns) -68: Performance: 98.992 0.242 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.015 199.6 -68: (ns/day) (hour/ns) -68: Performance: 50.321 0.477 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.069 0.035 199.5 -68: (ns/day) (hour/ns) -68: Performance: 22.454 1.069 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (80 ms) -68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (620 ms total) -68: -68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact -68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: MTTK coupling is deprecated and will soon be removed -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: MTTK coupling is deprecated and will soon be removed -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.047 0.024 199.7 -68: (ns/day) (hour/ns) -68: Performance: 61.776 0.389 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.059 0.030 199.7 -68: (ns/day) (hour/ns) -68: Performance: 26.133 0.918 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.030 0.015 199.5 -68: (ns/day) (hour/ns) -68: Performance: 52.528 0.457 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (83 ms) -68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (83 ms total) -68: -68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact -68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.032 0.016 199.4 -68: (ns/day) (hour/ns) -68: Performance: 92.411 0.260 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.017 199.3 -68: (ns/day) (hour/ns) -68: Performance: 44.779 0.536 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.031 0.016 199.3 -68: (ns/day) (hour/ns) -68: Performance: 49.357 0.486 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (63 ms) -68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'FirstWaterMolecule' has 3 atoms -68: Pull group 2 'SecondWaterMolecule' has 3 atoms -68: Number of degrees of freedom in T-Coupling group System is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 3 2 -68: 2 3 5 1.112 nm 1.000 nm -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps. -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.034 0.017 199.6 -68: (ns/day) (hour/ns) -68: Performance: 85.159 0.282 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.041 0.021 199.6 -68: (ns/day) (hour/ns) -68: Performance: 37.682 0.637 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.046 0.023 199.5 -68: (ns/day) (hour/ns) -68: Performance: 33.971 0.706 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) -68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (140 ms total) -68: -68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact -68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: Setting the AWH bias MC random seed to -8421633 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Setting the AWH bias MC random seed to -1065219 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.040 0.020 199.1 -68: (ns/day) (hour/ns) -68: Performance: 73.720 0.326 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.035 0.018 198.3 -68: (ns/day) (hour/ns) -68: Performance: 43.632 0.550 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.045 0.023 199.1 -68: (ns/day) (hour/ns) -68: Performance: 34.251 0.701 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (99 ms) -68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -68: Setting the AWH bias MC random seed to -100814089 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Setting the AWH bias MC random seed to 2143279070 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Pull group 1 'C_&_r_1' has 1 atoms -68: Pull group 2 'N_&_r_2' has 1 atoms -68: Pull group 3 'CA' has 1 atoms -68: Pull group 4 'C_&_r_2' has 1 atoms -68: Pull group 5 'N_&_r_3' has 1 atoms -68: Number of degrees of freedom in T-Coupling group System is 51.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: Pull group natoms pbc atom distance at start reference at t=0 -68: 1 1 0 -68: 2 1 0 179.098 deg 0.000 deg -68: 2 1 0 -68: 3 1 0 158.667 deg 0.000 deg -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps. -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2145 of the 2145 non-bonded parameter combinations -68: -68: Generated 2145 of the 2145 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.047 0.024 199.0 -68: (ns/day) (hour/ns) -68: Performance: 61.884 0.388 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.083 0.042 199.3 -68: (ns/day) (hour/ns) -68: Performance: 18.642 1.287 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Alanine-dipeptide' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.173 0.087 199.7 -68: (ns/day) (hour/ns) -68: Performance: 8.960 2.678 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (185 ms) -68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (284 ms total) -68: -68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact -68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group System is 79.00 -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps. -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: Generated 2485 of the 2485 non-bonded parameter combinations -68: -68: Generated 2485 of the 2485 1-4 parameter combinations -68: -68: Excluding 3 bonded neighbours molecule type 'nonanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.101 0.051 199.8 -68: (ns/day) (hour/ns) -68: Performance: 29.072 0.826 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 8 steps, 0.0 ps. -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.043 0.021 199.6 -68: (ns/day) (hour/ns) -68: Performance: 36.360 0.660 -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun '30 atom system in water' -68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.095 0.048 199.4 -68: (ns/day) (hour/ns) -68: Performance: 16.250 1.477 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (179 ms) -68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (179 ms total) -68: -68: [----------] 3 tests from Checking/InitialConstraintsTest -68: [ RUN ] Checking/InitialConstraintsTest.Works/0 -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -134521602 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.040 0.020 199.4 -68: (ns/day) (hour/ns) -68: Performance: 8.566 2.802 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (26 ms) -68: [ RUN ] Checking/InitialConstraintsTest.Works/1 -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -71437409 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.014 0.007 199.2 -68: (ns/day) (hour/ns) -68: Performance: 24.742 0.970 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (11 ms) -68: [ RUN ] Checking/InitialConstraintsTest.Works/2 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: Integrator method md-vv-avek is implemented primarily for validation -68: purposes; for molecular dynamics, you should probably be using md or -68: md-vv -68: -68: Number of degrees of freedom in T-Coupling group rest is 11.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 1141.954 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI thread -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -69271698 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: turning H bonds into constraints... -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: turning H bonds into constraints... -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.2 -68: (ns/day) (hour/ns) -68: Performance: 15.544 1.544 -68: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file -68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (16 ms) -68: [----------] 3 tests from Checking/InitialConstraintsTest (54 ms total) -68: -68: [----------] Global test environment tear-down -68: [==========] 76 tests from 13 test suites ran. (16960 ms total) -68: [ PASSED ] 76 tests. -68/92 Test #68: MdrunIOTests .............................. Passed 16.98 sec -test 69 - Start 69: MdrunTestsOneRank - -69: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" -69: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -69: Test timeout computed to be: 600 -69: [==========] Running 29 tests from 8 test suites. -69: [----------] Global test environment set-up. -69: [----------] 1 test from CompelTest -69: [ RUN ] CompelTest.SwapCanRun -69: Generating 1-4 interactions: fudge = 0.5 -69: Split0 group 'Ch0' contains 83 atoms. -69: Split1 group 'Ch1' contains 83 atoms. -69: Solvent group 'SOL' contains 11931 atoms. -69: Swap group 'NA+' contains 19 atoms. -69: Swap group 'CL-' contains 19 atoms. -69: Number of degrees of freedom in T-Coupling group System is 27869.00 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -69: Removing center of mass motion in the presence of position restraints -69: might cause artifacts. When you are using position restraints to -69: equilibrate a macro-molecule, the artifacts are usually negligible. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Update groups can not be used for this system because there are three or more consecutively coupled constraints -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: SWAP: Determining initial numbers of ions per compartment. -69: SWAP: Setting pointers for checkpoint writing -69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -69: starting mdrun 'Channel_coco in octane membrane' -69: 2 steps, 0.0 ps. -69: Setting the LD random seed to -2014323617 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: turning all bonds into constraints... -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: turning all bonds into constraints... -69: -69: Excluding 1 bonded neighbours molecule type 'NA' -69: -69: turning all bonds into constraints... -69: -69: Excluding 1 bonded neighbours molecule type 'CL' -69: -69: turning all bonds into constraints... -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning all bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -69: -69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 1 Mb of data -69: -69: Writing final coordinates. -69: -69: NOTE: 30 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.343 0.172 199.9 -69: (ns/day) (hour/ns) -69: Performance: 7.547 3.180 -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -69: -69: Update groups can not be used for this system because there are three or more consecutively coupled constraints -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: SWAP: Setting pointers for checkpoint writing -69: SWAP: Copying channel fluxes from checkpoint file data -69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -69: starting mdrun 'Channel_coco in octane membrane' -69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -69: -69: Writing final coordinates. -69: -69: NOTE: 20 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.246 0.123 199.9 -69: (ns/day) (hour/ns) -69: Performance: 10.545 2.276 -69: [ OK ] CompelTest.SwapCanRun (684 ms) -69: [----------] 1 test from CompelTest (684 ms total) -69: -69: [----------] 6 tests from BondedInteractionsTest -69: [ RUN ] BondedInteractionsTest.NormalBondWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 2 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 24 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 187.1 -69: (ns/day) (hour/ns) -69: Performance: 254.129 0.094 -69: Setting the LD random seed to 2063325815 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalBondWorks (6 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 2 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 21 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.000 0.000 184.5 -69: (ns/day) (hour/ns) -69: Performance: 319.566 0.075 -69: Setting the LD random seed to -33858697 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) -69: [ RUN ] BondedInteractionsTest.NormalAngleWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 24 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 185.3 -69: (ns/day) (hour/ns) -69: Performance: 289.447 0.083 -69: Setting the LD random seed to 1607191999 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalAngleWorks (9 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 23 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 186.9 -69: (ns/day) (hour/ns) -69: Performance: 234.707 0.102 -69: Setting the LD random seed to -1396745254 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (13 ms) -69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 22 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 185.8 -69: (ns/day) (hour/ns) -69: Performance: 302.242 0.079 -69: Setting the LD random seed to 2145763223 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (9 ms) -69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: -69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -69: In moleculetype 'butane' 4 atoms are not bound by a potential or -69: constraint to any other atom in the same moleculetype. Although -69: technically this might not cause issues in a simulation, this often means -69: that the user forgot to add a bond/potential/constraint or put multiple -69: molecules in the same moleculetype definition by mistake. Run with -v to -69: get information for each atom. -69: -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -69: -69: Reading frames from gro file 'A single butane', 4 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 21 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 184.6 -69: (ns/day) (hour/ns) -69: Performance: 303.000 0.079 -69: Setting the LD random seed to -275776557 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'butane' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (10 ms) -69: [----------] 6 tests from BondedInteractionsTest (54 ms total) -69: -69: [----------] 2 tests from BoxDeformationTest -69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Argon' -69: 0 steps, 0.0 ps. -69: -69: NOTE: 28 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.000 0.000 164.1 -69: (ns/day) (hour/ns) -69: Performance: 593.592 0.040 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -2099273 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: Setting gen_seed to 859567771 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (9 ms) -69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 1293.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 20 steps, 0.0 ps. -69: Setting the LD random seed to -1967654983 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -69: -69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.15 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.131 0.066 199.8 -69: (ns/day) (hour/ns) -69: Performance: 55.145 0.435 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (356 ms) -69: [----------] 2 tests from BoxDeformationTest (366 ms total) -69: -69: [----------] 1 test from PositionRestraintCommTest -69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: You have set rlist larger than the interaction cut-off, but you also have -69: verlet-buffer-tolerance > 0. Will set rlist using -69: verlet-buffer-tolerance. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (10) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: 13489 atoms are not part of any of the VCM groups -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: 13489 atoms are not part of any center of mass motion removal group. -69: This may lead to artifacts. -69: In most cases one should use one group for the whole system. -69: -69: Number of degrees of freedom in T-Coupling group System is 29527.73 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -69: Removing center of mass motion in the presence of position restraints -69: might cause artifacts. When you are using position restraints to -69: equilibrate a macro-molecule, the artifacts are usually negligible. -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Channel_coco in octane membrane' -69: 10 steps, 0.0 ps. -69: Setting the LD random seed to 2112342524 -69: -69: Generated 330891 of the 330891 non-bonded parameter combinations -69: -69: Generated 330891 of the 330891 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 1 bonded neighbours molecule type 'NA' -69: -69: Excluding 1 bonded neighbours molecule type 'CL' -69: -69: Excluding 3 bonded neighbours molecule type 'Protein' -69: -69: Excluding 3 bonded neighbours molecule type 'OCT' -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: Chain0: 2.207 2.168 7.330 -69: Chain1: 2.228 2.186 2.401 -69: Chain0: 2.207 2.168 7.330 -69: Chain1: 2.228 2.186 2.401 -69: -69: This run will generate roughly 1 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.357 0.179 199.9 -69: (ns/day) (hour/ns) -69: Performance: 10.630 2.258 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (527 ms) -69: [----------] 1 test from PositionRestraintCommTest (527 ms total) -69: -69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to 1593039935 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.090 0.045 199.5 -69: (ns/day) (hour/ns) -69: Performance: 9.619 2.495 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -541331722 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.110 0.055 199.6 -69: (ns/day) (hour/ns) -69: Performance: 7.869 3.050 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) -69: -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1108 ms) -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -1543701635 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.044 0.022 199.1 -69: (ns/day) (hour/ns) -69: Performance: 19.660 1.221 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 2 [file ala.top, line 256]: -69: For energy conservation with LINCS, lincs_iter should be 2 or larger. -69: -69: -69: Number of degrees of freedom in T-Coupling group rest is 54.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -69: The optimal PME mesh load for parallel simulations is below 0.5 -69: and for highly parallel simulations between 0.25 and 0.33, -69: for higher performance, increase the cut-off and the PME grid spacing. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -69: Can not increase nstlist because an NVE ensemble is used -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'UNNAMED in water' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -2113793 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -69: Calculating fourier grid dimensions for X Y Z -69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -69: -69: Estimate for the relative computational load of the PME mesh part: 0.94 -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.104 0.052 199.6 -69: (ns/day) (hour/ns) -69: Performance: 8.271 2.902 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (105 ms) -69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1214 ms total) -69: -69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Pull group 1 'FirstWaterMolecule' has 3 atoms -69: Pull group 2 'SecondWaterMolecule' has 3 atoms -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Pull group natoms pbc atom distance at start reference at t=0 -69: 1 3 2 -69: 2 3 5 1.112 nm 1.000 nm -69: -69: There was 1 NOTE -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -8814641 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.110 0.055 199.6 -69: (ns/day) (hour/ns) -69: Performance: 7.827 3.067 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Pull group 1 'FirstWaterMolecule' has 3 atoms -69: Pull group 2 'SecondWaterMolecule' has 3 atoms -69: Number of degrees of freedom in T-Coupling group rest is 9.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Pull group natoms pbc atom distance at start reference at t=0 -69: 1 3 2 -69: 2 3 5 1.112 nm 1.000 nm -69: -69: There was 1 NOTE -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -69: Can not increase nstlist because an NVE ensemble is used -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 4 steps, 0.0 ps. -69: Setting the LD random seed to -822083641 -69: -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.060 0.030 199.4 -69: (ns/day) (hour/ns) -69: Performance: 14.328 1.675 -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -69: -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -69: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (113 ms) -69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (113 ms total) -69: -69: [----------] 12 tests from FreezeWorks/FreezeGroupTest -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.056 0.028 199.5 -69: (ns/day) (hour/ns) -69: Performance: 27.557 0.871 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (45 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.057 0.029 199.4 -69: (ns/day) (hour/ns) -69: Performance: 27.254 0.881 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (39 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.077 0.039 199.6 -69: (ns/day) (hour/ns) -69: Performance: 20.074 1.196 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (54 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.120 0.060 199.8 -69: (ns/day) (hour/ns) -69: Performance: 12.908 1.859 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (76 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: NVE simulation: will use the initial temperature of 246.451 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 5 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.476 0.238 199.9 -69: (ns/day) (hour/ns) -69: Performance: 3.265 7.350 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (249 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped -69: Parrinello-Rahman is not implemented in md-vv. -69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.094 0.047 199.7 -69: (ns/day) (hour/ns) -69: Performance: 16.453 1.459 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (71 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.079 0.040 199.4 -69: (ns/day) (hour/ns) -69: Performance: 19.636 1.222 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (66 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.064 0.032 199.5 -69: (ns/day) (hour/ns) -69: Performance: 24.348 0.986 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (54 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.062 0.031 199.5 -69: (ns/day) (hour/ns) -69: Performance: 24.917 0.963 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (69 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.233 0.116 199.8 -69: (ns/day) (hour/ns) -69: Performance: 6.681 3.592 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (153 ms) -69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: There are 5 atoms that are fully frozen and part of COMM removal -69: group(s), removing these atoms from the COMM removal group(s) -69: -69: -69: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: There are 3 atoms that are frozen along less then 3 dimensions and part -69: of COMM removal group(s), due to limitations in the code these still -69: contribute to the mass of the COM along frozen dimensions and therefore -69: the COMM correction will be too small. -69: -69: Number of degrees of freedom in T-Coupling group System is 33.00 -69: -69: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 4 NOTEs -69: -69: There was 1 WARNING -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -69: -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Alanine-dipeptide' -69: 8 steps, 0.0 ps. -69: Generated 2145 of the 2145 non-bonded parameter combinations -69: -69: Generated 2145 of the 2145 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -69: -69: turning H bonds into constraints... -69: -69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -69: -69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.272 0.136 199.9 -69: (ns/day) (hour/ns) -69: Performance: 5.706 4.206 -69: -69: -69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (176 ms) -69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1058 ms total) -69: -69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -7671649 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.020 0.010 199.0 -69: (ns/day) (hour/ns) -69: Performance: 155.139 0.155 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (17 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because verlet-buffer-tolerance is not set or used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -275187018 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.028 0.014 199.2 -69: (ns/day) (hour/ns) -69: Performance: 109.222 0.220 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (18 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -1410203685 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.020 0.010 198.9 -69: (ns/day) (hour/ns) -69: Performance: 151.584 0.158 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (16 ms) -69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -69: that with the Verlet scheme, nstlist has no effect on the accuracy of -69: your simulation. -69: -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -69: < 0 -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (4) -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -69: Net Acceleration in X direction, will not be corrected -69: Net Acceleration in Y direction, will not be corrected -69: Net Acceleration in Z direction, will not be corrected -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -69: Can not increase nstlist because verlet-buffer-tolerance is not set or used -69: Using 1 MPI thread -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'spc2' -69: 8 steps, 0.0 ps. -69: Generated 3 of the 3 non-bonded parameter combinations -69: -69: Generated 3 of the 3 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Setting gen_seed to -1376256065 -69: -69: Velocities were taken from a Maxwell distribution at 0 K -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.875 0.437 200.0 -69: (ns/day) (hour/ns) -69: Performance: 3.555 6.751 -69: -69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (443 ms) -69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (495 ms total) -69: -69: [----------] Global test environment tear-down -69: [==========] 29 tests from 8 test suites ran. (4925 ms total) -69: [ PASSED ] 28 tests. -69: [ SKIPPED ] 1 test, listed below: -69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -69/92 Test #69: MdrunTestsOneRank ......................... Passed 4.94 sec -test 70 - Start 70: MdrunTestsTwoRanks - -70: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" -70: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -70: Test timeout computed to be: 600 -70: [==========] Running 29 tests from 8 test suites. -70: [----------] Global test environment set-up. -70: [----------] 1 test from CompelTest -70: [ RUN ] CompelTest.SwapCanRun -70: Generating 1-4 interactions: fudge = 0.5 -70: Split0 group 'Ch0' contains 83 atoms. -70: Split1 group 'Ch1' contains 83 atoms. -70: Solvent group 'SOL' contains 11931 atoms. -70: Swap group 'NA+' contains 19 atoms. -70: Swap group 'CL-' contains 19 atoms. -70: Number of degrees of freedom in T-Coupling group System is 27869.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -70: Removing center of mass motion in the presence of position restraints -70: might cause artifacts. When you are using position restraints to -70: equilibrate a macro-molecule, the artifacts are usually negligible. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Update groups can not be used for this system because there are three or more consecutively coupled constraints -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: SWAP: Determining initial numbers of ions per compartment. -70: SWAP: Setting pointers for checkpoint writing -70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -70: starting mdrun 'Channel_coco in octane membrane' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to -55394331 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: turning all bonds into constraints... -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: turning all bonds into constraints... -70: -70: Excluding 1 bonded neighbours molecule type 'NA' -70: -70: turning all bonds into constraints... -70: -70: Excluding 1 bonded neighbours molecule type 'CL' -70: -70: turning all bonds into constraints... -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 1 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 1.1%. -70: The balanceable part of the MD step is 26%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 0.3%. -70: -70: -70: NOTE: 5 % of the run time was spent in domain decomposition, -70: 24 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.463 0.116 399.6 -70: (ns/day) (hour/ns) -70: Performance: 11.174 2.148 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -70: -70: Update groups can not be used for this system because there are three or more consecutively coupled constraints -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: SWAP: Setting pointers for checkpoint writing -70: SWAP: Copying channel fluxes from checkpoint file data -70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -70: starting mdrun 'Channel_coco in octane membrane' -70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: NOTE: 15 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.322 0.081 399.5 -70: (ns/day) (hour/ns) -70: Performance: 16.055 1.495 -70: [ OK ] CompelTest.SwapCanRun (585 ms) -70: [----------] 1 test from CompelTest (585 ms total) -70: -70: [----------] 6 tests from BondedInteractionsTest -70: [ RUN ] BondedInteractionsTest.NormalBondWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 2 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 23 % of the run time was spent in domain decomposition, -70: 16 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.000 379.5 -70: (ns/day) (hour/ns) -70: Performance: 205.261 0.117 -70: Setting the LD random seed to -229473 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalBondWorks (6 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 2 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 10 % of the run time was spent in domain decomposition, -70: 7 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.004 0.001 390.8 -70: (ns/day) (hour/ns) -70: Performance: 91.362 0.263 -70: Setting the LD random seed to -34084610 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (7 ms) -70: [ RUN ] BondedInteractionsTest.NormalAngleWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 27 % of the run time was spent in domain decomposition, -70: 11 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.002 0.000 381.1 -70: (ns/day) (hour/ns) -70: Performance: 192.299 0.125 -70: Setting the LD random seed to -224412361 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalAngleWorks (7 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 23 % of the run time was spent in domain decomposition, -70: 16 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.001 0.000 379.1 -70: (ns/day) (hour/ns) -70: Performance: 220.096 0.109 -70: Setting the LD random seed to -302448659 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (6 ms) -70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: NOTE: 20 % of the run time was spent in domain decomposition, -70: 14 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.001 0.000 379.8 -70: (ns/day) (hour/ns) -70: Performance: 220.230 0.109 -70: Setting the LD random seed to -439354337 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (10 ms) -70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -70: In moleculetype 'butane' 4 atoms are not bound by a potential or -70: constraint to any other atom in the same moleculetype. Although -70: technically this might not cause issues in a simulation, this often means -70: that the user forgot to add a bond/potential/constraint or put multiple -70: molecules in the same moleculetype definition by mistake. Run with -v to -70: get information for each atom. -70: -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -70: NVE simulation with an initial temperature of zero: will use a Verlet -70: buffer of 10%. Check your energy drift! -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -70: -70: Reading frames from gro file 'A single butane', 4 atoms. -70: Reading frame 0 time 0.000 Last frame 0 time 0.000 -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.005 0.001 393.6 -70: (ns/day) (hour/ns) -70: Performance: 69.610 0.345 -70: Setting the LD random seed to -570490881 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'butane' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (7 ms) -70: [----------] 6 tests from BondedInteractionsTest (45 ms total) -70: -70: [----------] 2 tests from BoxDeformationTest -70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Number of degrees of freedom in T-Coupling group rest is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 0 steps, 0.0 ps. -70: -70: NOTE: 28 % of the run time was spent in domain decomposition, -70: 21 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.001 0.000 328.2 -70: (ns/day) (hour/ns) -70: Performance: 614.738 0.039 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -86279753 -70: -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Setting gen_seed to -1628017938 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (5 ms) -70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group rest is 1293.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 20 steps, 0.0 ps. -70: Setting the LD random seed to 333704171 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -70: -70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.15 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 1.9%. -70: The balanceable part of the MD step is 58%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 1.1%. -70: -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.101 0.025 398.9 -70: (ns/day) (hour/ns) -70: Performance: 143.213 0.168 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (313 ms) -70: [----------] 2 tests from BoxDeformationTest (319 ms total) -70: -70: [----------] 1 test from PositionRestraintCommTest -70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: You have set rlist larger than the interaction cut-off, but you also have -70: verlet-buffer-tolerance > 0. Will set rlist using -70: verlet-buffer-tolerance. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (10) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: 13489 atoms are not part of any of the VCM groups -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: 13489 atoms are not part of any center of mass motion removal group. -70: This may lead to artifacts. -70: In most cases one should use one group for the whole system. -70: -70: Number of degrees of freedom in T-Coupling group System is 29527.73 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -70: Removing center of mass motion in the presence of position restraints -70: might cause artifacts. When you are using position restraints to -70: equilibrate a macro-molecule, the artifacts are usually negligible. -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Channel_coco in octane membrane' -70: 10 steps, 0.0 ps. -70: Setting the LD random seed to 2011102198 -70: -70: Generated 330891 of the 330891 non-bonded parameter combinations -70: -70: Generated 330891 of the 330891 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 1 bonded neighbours molecule type 'NA' -70: -70: Excluding 1 bonded neighbours molecule type 'CL' -70: -70: Excluding 3 bonded neighbours molecule type 'Protein' -70: -70: Excluding 3 bonded neighbours molecule type 'OCT' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: Chain0: 2.207 2.168 7.330 -70: Chain1: 2.228 2.186 2.401 -70: Chain0: 2.207 2.168 7.330 -70: Chain1: 2.228 2.186 2.401 -70: -70: This run will generate roughly 1 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 15 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.460 0.115 399.6 -70: (ns/day) (hour/ns) -70: Performance: 16.501 1.454 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (473 ms) -70: [----------] 1 test from PositionRestraintCommTest (473 ms total) -70: -70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -708840545 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 49 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.513 0.128 399.7 -70: (ns/day) (hour/ns) -70: Performance: 3.367 7.129 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to 1979187197 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 49 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.221 0.055 399.2 -70: (ns/day) (hour/ns) -70: Performance: 7.798 3.078 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) -70: -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (493 ms) -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -1343330574 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.068 0.017 397.8 -70: (ns/day) (hour/ns) -70: Performance: 25.350 0.947 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 2 [file ala.top, line 256]: -70: For energy conservation with LINCS, lincs_iter should be 2 or larger. -70: -70: -70: Number of degrees of freedom in T-Coupling group rest is 54.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -70: The optimal PME mesh load for parallel simulations is below 0.5 -70: and for highly parallel simulations between 0.25 and 0.33, -70: for higher performance, increase the cut-off and the PME grid spacing. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -70: Can not increase nstlist because an NVE ensemble is used -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'UNNAMED in water' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -1164599683 -70: -70: Generated 2211 of the 2211 non-bonded parameter combinations -70: -70: Generated 2211 of the 2211 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -70: -70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -70: Calculating fourier grid dimensions for X Y Z -70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -70: -70: Estimate for the relative computational load of the PME mesh part: 0.94 -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.057 0.014 397.4 -70: (ns/day) (hour/ns) -70: Performance: 30.148 0.796 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (65 ms) -70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (559 ms total) -70: -70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -365985995 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 48 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.056 0.014 397.6 -70: (ns/day) (hour/ns) -70: Performance: 30.737 0.781 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -70: Can not increase nstlist because an NVE ensemble is used -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps. -70: Setting the LD random seed to -310917645 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 48 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.059 0.015 397.4 -70: (ns/day) (hour/ns) -70: Performance: 29.196 0.822 -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -70: -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (46 ms) -70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (46 ms total) -70: -70: [----------] 12 tests from FreezeWorks/FreezeGroupTest -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 14.6%. -70: The balanceable part of the MD step is 41%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 6.0%. -70: -70: NOTE: 6.0 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.044 0.011 395.9 -70: (ns/day) (hour/ns) -70: Performance: 70.705 0.339 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (24 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 14.9%. -70: The balanceable part of the MD step is 45%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 6.7%. -70: -70: NOTE: 6.7 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 42 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.029 0.007 396.7 -70: (ns/day) (hour/ns) -70: Performance: 107.697 0.223 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (20 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 13.6%. -70: The balanceable part of the MD step is 46%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 6.2%. -70: -70: NOTE: 6.2 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 42 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.027 0.007 395.0 -70: (ns/day) (hour/ns) -70: Performance: 113.199 0.212 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (19 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 18.5%. -70: The balanceable part of the MD step is 46%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 8.6%. -70: -70: NOTE: 8.6 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.061 0.015 398.4 -70: (ns/day) (hour/ns) -70: Performance: 50.752 0.473 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (26 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: NVE simulation: will use the initial temperature of 246.451 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 20.0%. -70: The balanceable part of the MD step is 48%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 9.5%. -70: -70: NOTE: 9.5 % of the available CPU time was lost due to load imbalance -70: in the domain decomposition. -70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) -70: You can also consider manually changing the decomposition (option -dd); -70: e.g. by using fewer domains along the box dimension in which there is -70: considerable inhomogeneity in the simulated system. -70: -70: NOTE: 43 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.029 0.007 397.6 -70: (ns/day) (hour/ns) -70: Performance: 105.903 0.227 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (18 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped -70: Parrinello-Rahman is not implemented in md-vv. -70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.030 0.008 397.6 -70: (ns/day) (hour/ns) -70: Performance: 101.995 0.235 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (21 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.032 0.008 397.6 -70: (ns/day) (hour/ns) -70: Performance: 96.957 0.248 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (22 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.039 0.010 397.9 -70: (ns/day) (hour/ns) -70: Performance: 79.775 0.301 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (25 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.042 0.011 398.3 -70: (ns/day) (hour/ns) -70: Performance: 73.864 0.325 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (45 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 45 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.034 0.009 397.6 -70: (ns/day) (hour/ns) -70: Performance: 91.443 0.262 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (43 ms) -70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: There are 5 atoms that are fully frozen and part of COMM removal -70: group(s), removing these atoms from the COMM removal group(s) -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: There are 3 atoms that are frozen along less then 3 dimensions and part -70: of COMM removal group(s), due to limitations in the code these still -70: contribute to the mass of the COM along frozen dimensions and therefore -70: the COMM correction will be too small. -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: There was 1 WARNING -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 -70: -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: NOTE: 46 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.039 0.010 398.2 -70: (ns/day) (hour/ns) -70: Performance: 79.318 0.303 -70: -70: -70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (42 ms) -70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (310 ms total) -70: -70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -572565618 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 10.2%. -70: The balanceable part of the MD step is 37%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 3.7%. -70: -70: -70: NOTE: 50 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.296 0.074 399.6 -70: (ns/day) (hour/ns) -70: Performance: 21.012 1.142 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (83 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because verlet-buffer-tolerance is not set or used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to 1873411932 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 9.4%. -70: The balanceable part of the MD step is 37%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 3.5%. -70: -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.045 0.011 397.1 -70: (ns/day) (hour/ns) -70: Performance: 138.376 0.173 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (24 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -1074048129 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 7.2%. -70: The balanceable part of the MD step is 42%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 3.0%. -70: -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.051 0.013 397.4 -70: (ns/day) (hour/ns) -70: Performance: 122.255 0.196 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (20 ms) -70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -70: < 0 -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -70: Net Acceleration in X direction, will not be corrected -70: Net Acceleration in Y direction, will not be corrected -70: Net Acceleration in Z direction, will not be corrected -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -70: Can not increase nstlist because verlet-buffer-tolerance is not set or used -70: Using 2 MPI threads -70: Using 2 OpenMP threads per tMPI thread -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Setting gen_seed to -407011337 -70: -70: Velocities were taken from a Maxwell distribution at 0 K -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: -70: Dynamic load balancing report: -70: DLB was off during the run due to low measured imbalance. -70: Average load imbalance: 4.8%. -70: The balanceable part of the MD step is 44%, load imbalance is computed from this. -70: Part of the total run time spent waiting due to load imbalance: 2.1%. -70: -70: -70: NOTE: 47 % of the run time was spent communicating energies, -70: you might want to increase some nst* mdp options -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.050 0.013 397.5 -70: (ns/day) (hour/ns) -70: Performance: 122.524 0.196 -70: -70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (21 ms) -70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (151 ms total) -70: -70: [----------] Global test environment tear-down -70: [==========] 29 tests from 8 test suites ran. (2735 ms total) -70: [ PASSED ] 28 tests. -70: [ SKIPPED ] 1 test, listed below: -70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 2.75 sec -test 71 - Start 71: MdrunSingleRankAlgorithmsTests - -71: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" -71: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -71: Test timeout computed to be: 600 -71: [==========] Running 5 tests from 3 test suites. -71: [----------] Global test environment set-up. -71: [----------] 1 test from DispersionCorrectionTest -71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun -71: Generating 1-4 interactions: fudge = 0.5 -71: Number of degrees of freedom in T-Coupling group System is 30.00 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -71: There are 9 non-linear virtual site constructions. Their contribution to -71: the energy error is approximated. In most cases this does not affect the -71: error significantly. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 2 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -71: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 -71: -71: Update groups can not be used for this system because an incompatible virtual site type is used -71: -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine dipeptide in vacuo' -71: 200 steps, 0.4 ps. -71: Setting the LD random seed to 1539035071 -71: -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -71: -71: Cleaning up constraints and constant bonded interactions with virtual sites -71: -71: Converted 3 Bonds with virtual sites to connections, 7 left -71: -71: Removed 18 Angles with virtual sites, 21 left -71: -71: Removed 10 Proper Dih.s with virtual sites, 44 left -71: -71: Converted 12 Constraints with virtual sites to connections, 0 left -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -71: -71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.043 0.022 199.4 -71: (ns/day) (hour/ns) -71: Performance: 1594.570 0.015 -71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (54 ms) -71: [----------] 1 test from DispersionCorrectionTest (54 ms total) -71: -71: [----------] 1 test from OriresTest -71: [ RUN ] OriresTest.OriresCanRun -71: Generating 1-4 interactions: fudge = 0.5 -71: Number of degrees of freedom in T-Coupling group System is 518.00 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There was 1 NOTE -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. -71: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 -71: -71: -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' -71: 10 steps, 0.0 ps. -71: Setting the LD random seed to 956956643 -71: -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/orires_1lvz.gro' -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -71: -71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.059 0.030 199.5 -71: (ns/day) (hour/ns) -71: Performance: 64.403 0.373 -71: [ OK ] OriresTest.OriresCanRun (616 ms) -71: [----------] 1 test from OriresTest (616 ms total) -71: -71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 -71: Number of degrees of freedom in T-Coupling group rest is 10.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 2 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Dipoles' -71: 20 steps, 0.1 ps. -71: Setting the LD random seed to 1662451284 -71: -71: Generated 1 of the 1 non-bonded parameter combinations -71: -71: Excluding 1 bonded neighbours molecule type 'Dipole' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -71: -71: Searching the wall atom type(s) -71: -71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 -71: -71: Estimate for the relative computational load of the PME mesh part: 1.00 -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.129 0.065 199.7 -71: (ns/day) (hour/ns) -71: Performance: 70.156 0.342 -71: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) -71: -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (546 ms) -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 -71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. -71: The supported numbers are > 1. -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) -71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: With epsilon_surface > 0 all molecules should be neutral. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: With epsilon_surface > 0 you can only use domain decomposition when there -71: are only small molecules with all bonds constrained (mdrun will check for -71: this). -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 4 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI thread -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Dipoles' -71: 20 steps, 0.1 ps. -71: Setting the LD random seed to 1065340731 -71: -71: Generated 1 of the 1 non-bonded parameter combinations -71: -71: Excluding 1 bonded neighbours molecule type 'Dipole' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -71: -71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 -71: -71: Estimate for the relative computational load of the PME mesh part: 1.00 -71: -71: This run will generate roughly 0 Mb of data -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.031 0.016 199.2 -71: (ns/day) (hour/ns) -71: Performance: 290.908 0.083 -71: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 -71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (193 ms) -71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (740 ms total) -71: -71: [----------] Global test environment tear-down -71: [==========] 5 tests from 3 test suites ran. (1495 ms total) -71: [ PASSED ] 5 tests. -71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 1.51 sec -test 72 - Start 72: Minimize1RankTests - -72: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" -72: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -72: Test timeout computed to be: 600 -72: [==========] Running 12 tests from 2 test suites. -72: [----------] Global test environment set-up. -72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -4.79910463671045e+01 -72: Maximum force = 1.86297359432219e+02 on atom 13 -72: Norm of force = 8.77219865482097e+01 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (288 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 3.02331e+02 on atom 3 -72: F-Norm = 1.18024e+02 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -5.58622538633256e+01 -72: Maximum force = 4.27274822366624e+02 on atom 13 -72: Norm of force = 1.84530029253875e+02 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (317 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 22.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 3.19376899751521e+02 -72: Maximum force = 9.99884921009767e+03 on atom 9 -72: Norm of force = 4.61669565054298e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: turning H bonds into constraints... -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (68 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: -72: NOTE 3 [file glycine_vacuo.top, line 12]: -72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -72: -72: Number of degrees of freedom in T-Coupling group System is 22.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 5 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 2.41575e+04 on atom 10 -72: F-Norm = 1.18451e+04 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 1.51743018140930e+02 -72: Maximum force = 7.42089573409109e+03 on atom 9 -72: Norm of force = 3.56929298615740e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: turning H bonds into constraints... -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (59 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: NOTE 3 [file unknown]: -72: You are using constraints on all bonds, whereas the forcefield has been -72: parametrized only with constraints involving hydrogen atoms. We suggest -72: using constraints = h-bonds instead, this will also improve performance. -72: -72: Number of degrees of freedom in T-Coupling group System is 23.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 5 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Update groups can not be used for this system because an incompatible virtual site type is used -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -1.56984193848274e+02 -72: Maximum force = 4.56923624626205e+02 on atom 17 -72: Norm of force = 1.83258377168315e+02 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -72: -72: turning all bonds into constraints... -72: -72: Cleaning up constraints and constant bonded interactions with virtual sites -72: -72: Removed 18 Angles with virtual sites, 21 left -72: -72: Removed 10 Proper Dih.s with virtual sites, 44 left -72: -72: Converted 15 Constraints with virtual sites to connections, 7 left -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (25 ms) -72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: NOTE 3 [file unknown]: -72: You are using constraints on all bonds, whereas the forcefield has been -72: parametrized only with constraints involving hydrogen atoms. We suggest -72: using constraints = h-bonds instead, this will also improve performance. -72: -72: -72: NOTE 4 [file unknown]: -72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -72: -72: Number of degrees of freedom in T-Coupling group System is 23.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 6 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Update groups can not be used for this system because an incompatible virtual site type is used -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 1.06800e+03 on atom 28 -72: F-Norm = 4.26922e+02 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = -1.69410778678182e+02 -72: Maximum force = 2.18225948474131e+02 on atom 17 -72: Norm of force = 7.92068036537818e+01 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -72: -72: turning all bonds into constraints... -72: -72: Cleaning up constraints and constant bonded interactions with virtual sites -72: -72: Removed 18 Angles with virtual sites, 21 left -72: -72: Removed 10 Proper Dih.s with virtual sites, 44 left -72: -72: Converted 15 Constraints with virtual sites to connections, 7 left -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (41 ms) -72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (801 ms total) -72: -72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents converged to Fmax < 10 in 1 steps -72: Potential Energy = -9.74257075835447e-01 -72: Maximum force = 4.01322929015133e+00 on atom 1 -72: Norm of force = 1.63839399694378e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (5 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 4.01323e+00 on atom 1 -72: F-Norm = 1.63839e+00 -72: -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -72: Potential Energy = -9.90642313893957e-01 -72: Maximum force = 2.57812909491104e+00 on atom 1 -72: Norm of force = 1.05251679559258e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (6 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 3 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Low-Memory BFGS Minimizer: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: Using 10 BFGS correction steps. -72: -72: F-max = 4.01323e+00 on atom 1 -72: F-Norm = 1.63839e+00 -72: -72: -72: writing lowest energy coordinates. -72: -72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps -72: Potential Energy = -9.90642313893957e-01 -72: Maximum force = 2.57812909491104e+00 on atom 1 -72: Norm of force = 1.05251679559258e+00 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (5 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Steepest Descents: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Steepest Descents did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 3.19395484891520e+02 -72: Maximum force = 9.97041707197911e+03 on atom 9 -72: Norm of force = 4.62274878665467e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (60 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Polak-Ribiere Conjugate Gradients: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: F-max = 2.41672e+04 on atom 10 -72: F-Norm = 1.19357e+04 -72: -72: -72: Energy minimization reached the maximum number of steps before the forces -72: reached the requested precision Fmax < 10. -72: -72: writing lowest energy coordinates. -72: -72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -72: Potential Energy = 1.56258793899481e+02 -72: Maximum force = 7.50181017480396e+03 on atom 9 -72: Norm of force = 3.61390332564874e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (60 ms) -72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -72: setting nstcomm equal to nstcalcenergy for less overhead -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -72: -72: Generating 1-4 interactions: fudge = 1 -72: Number of degrees of freedom in T-Coupling group System is 27.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -72: COM removal frequency is set to (4). -72: Other settings require a global communication frequency of 100. -72: Note that this will require additional global communication steps, -72: which will reduce performance when using multiple ranks. -72: Consider setting nstcomm to a multiple of 100. -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. -72: -72: Using 1 MPI thread -72: Using 2 OpenMP threads -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: -72: Low-Memory BFGS Minimizer: -72: Tolerance (Fmax) = 1.00000e+01 -72: Number of steps = 4 -72: Using 10 BFGS correction steps. -72: -72: F-max = 2.41672e+04 on atom 10 -72: F-Norm = 1.19357e+04 -72: -72: -72: Energy minimization has stopped, but the forces have not converged to the -72: requested precision Fmax < 10 (which may not be possible for your system). It -72: stopped because the algorithm tried to make a new step whose size was too -72: small, or there was no change in the energy since last step. Either way, we -72: regard the minimization as converged to within the available machine -72: precision, given your starting configuration and EM parameters. -72: -72: writing lowest energy coordinates. -72: -72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, -72: but did not reach the requested Fmax < 10. -72: Potential Energy = 5.61116097794205e+02 -72: Maximum force = 1.26854826291223e+04 on atom 10 -72: Norm of force = 6.06436286976271e+03 -72: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -72: -72: Generated 17396 of the 20503 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Glycine' -72: -72: This run will generate roughly 0 Mb of data -72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (60 ms) -72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (199 ms total) -72: -72: [----------] Global test environment tear-down -72: [==========] 12 tests from 2 test suites ran. (1065 ms total) -72: [ PASSED ] 12 tests. -72/92 Test #72: Minimize1RankTests ........................ Passed 1.08 sec -test 73 - Start 73: Minimize2RankTests - -73: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" -73: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -73: Test timeout computed to be: 600 -73: [==========] Running 12 tests from 2 test suites. -73: [----------] Global test environment set-up. -73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -4.79910463671047e+01 -73: Maximum force = 1.86297359432218e+02 on atom 13 -73: Norm of force = 8.77219865482097e+01 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -73: -73: Generated 330891 of the 330891 1-4 parameter combinations -73: -73: Excluding 2 bonded neighbours molecule type 'SOL' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (286 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 3.02331e+02 on atom 3 -73: F-Norm = 1.18024e+02 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -5.58622538633258e+01 -73: Maximum force = 4.27274822366617e+02 on atom 13 -73: Norm of force = 1.84530029253872e+02 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations -73: -73: Generated 330891 of the 330891 1-4 parameter combinations -73: -73: Excluding 2 bonded neighbours molecule type 'SOL' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (274 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 22.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 3.19376899751522e+02 -73: Maximum force = 9.99884921009767e+03 on atom 9 -73: Norm of force = 4.61669565054298e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: turning H bonds into constraints... -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (62 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: -73: NOTE 3 [file glycine_vacuo.top, line 12]: -73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -73: -73: Number of degrees of freedom in T-Coupling group System is 22.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 5 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 2.41575e+04 on atom 10 -73: F-Norm = 1.18451e+04 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 1.51743018140930e+02 -73: Maximum force = 7.42089573409109e+03 on atom 9 -73: Norm of force = 3.56929298615740e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: turning H bonds into constraints... -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (61 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: -73: NOTE 3 [file unknown]: -73: You are using constraints on all bonds, whereas the forcefield has been -73: parametrized only with constraints involving hydrogen atoms. We suggest -73: using constraints = h-bonds instead, this will also improve performance. -73: -73: Number of degrees of freedom in T-Coupling group System is 23.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 5 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Update groups can not be used for this system because an incompatible virtual site type is used -73: -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -1.56984193848274e+02 -73: Maximum force = 4.56923624626205e+02 on atom 17 -73: Norm of force = 1.83258377168315e+02 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -73: -73: turning all bonds into constraints... -73: -73: Cleaning up constraints and constant bonded interactions with virtual sites -73: -73: Removed 18 Angles with virtual sites, 21 left -73: -73: Removed 10 Proper Dih.s with virtual sites, 44 left -73: -73: Converted 15 Constraints with virtual sites to connections, 7 left -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (11 ms) -73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 0.5 -73: -73: NOTE 3 [file unknown]: -73: You are using constraints on all bonds, whereas the forcefield has been -73: parametrized only with constraints involving hydrogen atoms. We suggest -73: using constraints = h-bonds instead, this will also improve performance. -73: -73: -73: NOTE 4 [file unknown]: -73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -73: -73: Number of degrees of freedom in T-Coupling group System is 23.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 6 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Update groups can not be used for this system because an incompatible virtual site type is used -73: -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 1.06800e+03 on atom 28 -73: F-Norm = 4.26922e+02 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = -1.69410778678182e+02 -73: Maximum force = 2.18225948474131e+02 on atom 17 -73: Norm of force = 7.92068036537818e+01 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -73: -73: turning all bonds into constraints... -73: -73: Cleaning up constraints and constant bonded interactions with virtual sites -73: -73: Removed 18 Angles with virtual sites, 21 left -73: -73: Removed 10 Proper Dih.s with virtual sites, 44 left -73: -73: Converted 15 Constraints with virtual sites to connections, 7 left -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (13 ms) -73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (710 ms total) -73: -73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents converged to Fmax < 10 in 1 steps -73: Potential Energy = -9.74257075835447e-01 -73: Maximum force = 4.01322929015133e+00 on atom 3 -73: Norm of force = 1.63839399694378e+00 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (17 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 4.01323e+00 on atom 3 -73: F-Norm = 1.63839e+00 -73: -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -73: Potential Energy = -9.90642313893957e-01 -73: Maximum force = 2.57812909491104e+00 on atom 3 -73: Norm of force = 1.05251679559258e+00 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (7 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: -73: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -73: -73: Number of degrees of freedom in T-Coupling group System is 33.00 -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 3 NOTEs -73: -73: There was 1 WARNING -73: Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Argon' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Steepest Descents: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Steepest Descents did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 3.19395484891520e+02 -73: Maximum force = 9.97041707197911e+03 on atom 9 -73: Norm of force = 4.62274878665467e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (64 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -73: Using 2 MPI threads -73: Using 2 OpenMP threads per tMPI thread -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: -73: Polak-Ribiere Conjugate Gradients: -73: Tolerance (Fmax) = 1.00000e+01 -73: Number of steps = 4 -73: F-max = 2.41672e+04 on atom 10 -73: F-Norm = 1.19357e+04 -73: -73: -73: Energy minimization reached the maximum number of steps before the forces -73: reached the requested precision Fmax < 10. -73: -73: writing lowest energy coordinates. -73: -73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -73: Potential Energy = 1.56258793899481e+02 -73: Maximum force = 7.50181017480396e+03 on atom 9 -73: Norm of force = 3.61390332564874e+03 -73: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (61 ms) -73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -73: that with the Verlet scheme, nstlist has no effect on the accuracy of -73: your simulation. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -73: setting nstcomm equal to nstcalcenergy for less overhead -73: -73: -73: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -73: -73: Generating 1-4 interactions: fudge = 1 -73: Number of degrees of freedom in T-Coupling group System is 27.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -73: COM removal frequency is set to (4). -73: Other settings require a global communication frequency of 100. -73: Note that this will require additional global communication steps, -73: which will reduce performance when using multiple ranks. -73: Consider setting nstcomm to a multiple of 100. -73: -73: -73: There were 4 NOTEs -73: -73: There was 1 WARNING -73: Generated 20503 of the 20503 non-bonded parameter combinations -73: -73: Generated 17396 of the 20503 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Glycine' -73: -73: This run will generate roughly 0 Mb of data -73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (55 ms) -73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (210 ms total) -73: -73: [----------] Global test environment tear-down -73: [==========] 12 tests from 2 test suites ran. (978 ms total) -73: [ PASSED ] 12 tests. -73/92 Test #73: Minimize2RankTests ........................ Passed 0.99 sec -test 74 - Start 74: MdrunNonIntegratorTests - -74: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" -74: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -74: Test timeout computed to be: 600 -74: [==========] Running 53 tests from 5 test suites. -74: [----------] Global test environment set-up. -74: [----------] 1 test from NonbondedBenchTest -74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest -74: SIMD width: 2 -74: System size: 3000 atoms -74: Cut-off radius: 1 nm -74: Number of threads: 1 -74: Number of iterations: 1 -74: Compute energies: no -74: Ewald excl. corr.: analytical -74: -74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle -74: total useful -74: Ewald all geom. 4xM 26.360 26.3602 0.0402 0.0239 -74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (31 ms) -74: [----------] 1 test from NonbondedBenchTest (31 ms total) -74: -74: [----------] 5 tests from NormalModesWorks/NormalModesTest -74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 15.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Small system size (N=6), using full Hessian format. -74: Allocating Hessian memory... -74: -74: starting normal mode calculation '2 scaled waters' -74: 12 steps. -74: -74: Maximum force: 9.96989e-06 -74: -74: -74: Writing Hessian... -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading double precision matrix generated by GROMACS 2025.3-Debian_2025.3_1 -74: -74: Diagonalizing to find vectors 7 through 18... -74: Writing eigenvalues... -74: -74: Writing average structure & eigenvectors 7--18 to eigenvec.trr -74: Generated 3 of the 3 non-bonded parameter combinations -74: -74: Generated 3 of the 3 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: This run will generate roughly 0 Mb of data -74: There are: 6 Atoms -74: Using begin = 7 and end = 18 -74: Full matrix storage format, nrow=18, ncols=18 -74: Writing eigenfrequencies - negative eigenvalues will be set to zero. -74: Cannot compute entropy when -first = 7 -74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (8 ms) -74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 1 -74: -74: NOTE 3 [file villin.top, line 2452]: -74: System has non-zero total charge: -2.000000 -74: Total charge should normally be an integer. See -74: https://manual.gromacs.org/current/user-guide/floating-point.html -74: for discussion on how close it should be to an integer. -74: -74: -74: -74: Number of degrees of freedom in T-Coupling group System is 765.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 5 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Small system size (N=256), using full Hessian format. -74: Allocating Hessian memory... -74: -74: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' -74: 512 steps. -74: -74: Maximum force: 6.97568e-04 -74: -74: -74: Writing Hessian... -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading double precision matrix generated by GROMACS 2025.3-Debian_2025.3_1 -74: -74: Diagonalizing to find vectors 7 through 50... -74: Writing eigenvalues... -74: -74: Writing average structure & eigenvectors 7--50 to eigenvec.trr -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -74: -74: This run will generate roughly 0 Mb of data -74: There are: 256 Atoms -74: Using begin = 7 and end = 50 -74: Full matrix storage format, nrow=768, ncols=768 -74: Writing eigenfrequencies - negative eigenvalues will be set to zero. -74: Cannot compute entropy when -first = 7 -74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (780 ms) -74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 15.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Small system size (N=6), using full Hessian format. -74: Allocating Hessian memory... -74: -74: starting normal mode calculation 'flex spc dimer' -74: 12 steps. -74: -74: Maximum force: 3.36401e-04 -74: -74: -74: Writing Hessian... -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading double precision matrix generated by GROMACS 2025.3-Debian_2025.3_1 -74: -74: Diagonalizing to find vectors 7 through 18... -74: Writing eigenvalues... -74: -74: Writing average structure & eigenvectors 7--18 to eigenvec.trr -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: This run will generate roughly 0 Mb of data -74: There are: 6 Atoms -74: Using begin = 7 and end = 18 -74: Full matrix storage format, nrow=18, ncols=18 -74: Writing eigenfrequencies - negative eigenvalues will be set to zero. -74: Cannot compute entropy when -first = 7 -74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (289 ms) -74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 6.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Small system size (N=3), using full Hessian format. -74: Allocating Hessian memory... -74: -74: starting normal mode calculation '1 TIP5P' -74: 6 steps. -74: -74: Maximum force: 2.42882e-04 -74: -74: -74: Writing Hessian... -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading double precision matrix generated by GROMACS 2025.3-Debian_2025.3_1 -74: -74: Diagonalizing to find vectors 7 through 9... -74: Writing eigenvalues... -74: -74: Writing average structure & eigenvectors 7--9 to eigenvec.trr -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: This run will generate roughly 0 Mb of data -74: There are: 3 Atoms -74: There are: 2 VSites -74: Using begin = 7 and end = 9 -74: Full matrix storage format, nrow=9, ncols=9 -74: Writing eigenfrequencies - negative eigenvalues will be set to zero. -74: Cannot compute entropy when -first = 7 -74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (272 ms) -74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: Number of degrees of freedom in T-Coupling group System is 15.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 2 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Small system size (N=6), using full Hessian format. -74: Allocating Hessian memory... -74: -74: starting normal mode calculation 'sw dimer' -74: 12 steps. -74: -74: Maximum force: 1.07599e-03 -74: The force is probably not small enough to ensure that you are at a minimum. -74: Be aware that negative eigenvalues may occur -74: when the resulting matrix is diagonalized. -74: -74: -74: Writing Hessian... -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Reading double precision matrix generated by GROMACS 2025.3-Debian_2025.3_1 -74: -74: Diagonalizing to find vectors 7 through 18... -74: Writing eigenvalues... -74: -74: Writing average structure & eigenvectors 7--18 to eigenvec.trr -74: Generated 6 of the 10 non-bonded parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SW' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: This run will generate roughly 0 Mb of data -74: There are: 6 Atoms -74: There are: 2 Shells -74: There are: 2 VSites -74: -74: NOTE: in the current version shell prediction during the crun is disabled -74: -74: Using begin = 7 and end = 18 -74: Full matrix storage format, nrow=18, ncols=18 -74: Writing eigenfrequencies - negative eigenvalues will be set to zero. -74: Cannot compute entropy when -first = 7 -74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (7 ms) -74: [----------] 5 tests from NormalModesWorks/NormalModesTest (1358 ms total) -74: -74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -74: NVE simulation: will use the initial temperature of 68.810 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.017 0.009 199.1 -74: (ns/day) (hour/ns) -74: Performance: 168.617 0.142 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' -74: -74: trr version: GMX_trn_file (double precision) -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 23 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 194.1 -74: (ns/day) (hour/ns) -74: Performance: 2115.589 0.011 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (17 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -74: NVE simulation: will use the initial temperature of 68.810 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.022 0.011 199.5 -74: (ns/day) (hour/ns) -74: Performance: 132.918 0.181 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.7 -74: (ns/day) (hour/ns) -74: Performance: 2292.740 0.010 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (19 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: There were 2 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.019 0.009 199.3 -74: (ns/day) (hour/ns) -74: Performance: 154.925 0.155 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.7 -74: (ns/day) (hour/ns) -74: Performance: 2246.752 0.011 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (101 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: There were 2 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Argon' -74: 16 steps, 0.0 ps. -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.338 0.169 199.9 -74: (ns/day) (hour/ns) -74: Performance: 8.678 2.765 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 23 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.9 -74: (ns/day) (hour/ns) -74: Performance: 2136.869 0.011 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (178 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: NVE simulation: will use the initial temperature of 398.997 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.021 0.011 199.0 -74: (ns/day) (hour/ns) -74: Performance: 138.300 0.174 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 26 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.8 -74: (ns/day) (hour/ns) -74: Performance: 2021.856 0.012 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (290 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: NVE simulation: will use the initial temperature of 398.997 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 199.5 -74: (ns/day) (hour/ns) -74: Performance: 99.281 0.242 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 22 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.0 -74: (ns/day) (hour/ns) -74: Performance: 2124.343 0.011 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (303 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.022 0.011 198.9 -74: (ns/day) (hour/ns) -74: Performance: 133.908 0.179 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.001 0.001 193.4 -74: (ns/day) (hour/ns) -74: Performance: 1998.246 0.012 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (298 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'spc2' -74: 16 steps, 0.0 ps. -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.021 0.010 199.0 -74: (ns/day) (hour/ns) -74: Performance: 141.528 0.170 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 14 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 195.8 -74: (ns/day) (hour/ns) -74: Performance: 1277.336 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (401 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: NVE simulation: will use the initial temperature of 456.887 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 6 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.026 0.013 199.0 -74: (ns/day) (hour/ns) -74: Performance: 114.545 0.210 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 19 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 195.3 -74: (ns/day) (hour/ns) -74: Performance: 1292.342 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (34 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: NVE simulation: will use the initial temperature of 456.887 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 6 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 199.2 -74: (ns/day) (hour/ns) -74: Performance: 90.773 0.264 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 194.7 -74: (ns/day) (hour/ns) -74: Performance: 1501.851 0.016 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (34 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 5 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.015 0.007 198.3 -74: (ns/day) (hour/ns) -74: Performance: 199.533 0.120 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 21 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.002 0.001 193.9 -74: (ns/day) (hour/ns) -74: Performance: 1232.612 0.019 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (96 ms) -74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: There are 9 non-linear virtual site constructions. Their contribution to -74: the energy error is approximated. In most cases this does not affect the -74: error significantly. -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 5 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'Alanine dipeptide in vacuo' -74: 16 steps, 0.0 ps. -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.048 0.024 199.3 -74: (ns/day) (hour/ns) -74: Performance: 60.492 0.397 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 -74: -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.001 195.1 -74: (ns/day) (hour/ns) -74: Performance: 986.958 0.024 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (93 ms) -74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1870 ms total) -74: -74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.040 0.020 198.0 -74: (ns/day) (hour/ns) -74: Performance: 72.407 0.331 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.036 0.018 195.5 -74: (ns/day) (hour/ns) -74: Performance: 80.656 0.298 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (100 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.032 0.016 198.5 -74: (ns/day) (hour/ns) -74: Performance: 91.255 0.263 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 13 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.019 0.010 196.9 -74: (ns/day) (hour/ns) -74: Performance: 148.738 0.161 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (80 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.052 0.026 198.6 -74: (ns/day) (hour/ns) -74: Performance: 56.038 0.428 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 14 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.006 0.003 177.2 -74: (ns/day) (hour/ns) -74: Performance: 445.323 0.054 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (113 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.049 0.025 198.9 -74: (ns/day) (hour/ns) -74: Performance: 59.830 0.401 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.049 0.025 198.7 -74: (ns/day) (hour/ns) -74: Performance: 59.681 0.402 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (1862 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.047 0.024 196.6 -74: (ns/day) (hour/ns) -74: Performance: 61.259 0.392 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 10 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.004 123.6 -74: (ns/day) (hour/ns) -74: Performance: 406.157 0.059 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (104 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: NOTE: 17 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.097 0.048 199.2 -74: (ns/day) (hour/ns) -74: Performance: 30.292 0.792 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.012 0.007 183.5 -74: (ns/day) (hour/ns) -74: Performance: 225.267 0.107 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (104 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.047 0.024 199.0 -74: (ns/day) (hour/ns) -74: Performance: 62.082 0.387 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 18 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 188.3 -74: (ns/day) (hour/ns) -74: Performance: 749.829 0.032 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (50 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.039 0.020 198.8 -74: (ns/day) (hour/ns) -74: Performance: 73.966 0.324 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.009 0.005 185.3 -74: (ns/day) (hour/ns) -74: Performance: 297.541 0.081 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (58 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.069 0.035 199.3 -74: (ns/day) (hour/ns) -74: Performance: 42.384 0.566 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 18 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 188.7 -74: (ns/day) (hour/ns) -74: Performance: 765.291 0.031 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (95 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 198.5 -74: (ns/day) (hour/ns) -74: Performance: 97.560 0.246 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 183.9 -74: (ns/day) (hour/ns) -74: Performance: 687.336 0.035 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (53 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.070 0.035 199.3 -74: (ns/day) (hour/ns) -74: Performance: 41.875 0.573 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 184.4 -74: (ns/day) (hour/ns) -74: Performance: 726.314 0.033 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (169 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 2.937 1.468 200.0 -74: (ns/day) (hour/ns) -74: Performance: 1.000 23.993 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 20 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 185.8 -74: (ns/day) (hour/ns) -74: Performance: 857.782 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (1573 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.057 0.028 199.6 -74: (ns/day) (hour/ns) -74: Performance: 51.560 0.465 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 17 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 183.6 -74: (ns/day) (hour/ns) -74: Performance: 918.395 0.026 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (62 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.192 0.096 199.9 -74: (ns/day) (hour/ns) -74: Performance: 15.256 1.573 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 40 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.077 0.071 108.2 -74: (ns/day) (hour/ns) -74: Performance: 20.682 1.160 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (376 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.056 0.028 199.5 -74: (ns/day) (hour/ns) -74: Performance: 52.526 0.457 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 15 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 172.6 -74: (ns/day) (hour/ns) -74: Performance: 881.218 0.027 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (77 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: NOTE: 13 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.104 0.052 199.6 -74: (ns/day) (hour/ns) -74: Performance: 28.243 0.850 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.012 0.006 191.9 -74: (ns/day) (hour/ns) -74: Performance: 238.875 0.100 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (117 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.059 0.030 198.0 -74: (ns/day) (hour/ns) -74: Performance: 49.177 0.488 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 11 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.007 0.004 182.8 -74: (ns/day) (hour/ns) -74: Performance: 409.097 0.059 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (108 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.047 0.024 199.4 -74: (ns/day) (hour/ns) -74: Performance: 62.007 0.387 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 186.1 -74: (ns/day) (hour/ns) -74: Performance: 842.878 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (100 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.117 0.059 199.8 -74: (ns/day) (hour/ns) -74: Performance: 25.039 0.958 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 17 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 184.0 -74: (ns/day) (hour/ns) -74: Performance: 887.438 0.027 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (135 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.058 0.029 199.6 -74: (ns/day) (hour/ns) -74: Performance: 50.223 0.478 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 181.5 -74: (ns/day) (hour/ns) -74: Performance: 847.749 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (81 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.047 0.024 199.5 -74: (ns/day) (hour/ns) -74: Performance: 62.424 0.384 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 186.8 -74: (ns/day) (hour/ns) -74: Performance: 916.755 0.026 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (57 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: NVE simulation: will use the initial temperature of 294.908 K for -74: determining the Verlet buffer size -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 4 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.348 0.174 199.9 -74: (ns/day) (hour/ns) -74: Performance: 8.427 2.848 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 18 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 172.0 -74: (ns/day) (hour/ns) -74: Performance: 764.152 0.031 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (236 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.055 0.028 199.0 -74: (ns/day) (hour/ns) -74: Performance: 52.821 0.454 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 188.2 -74: (ns/day) (hour/ns) -74: Performance: 909.179 0.026 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (81 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.030 0.015 198.5 -74: (ns/day) (hour/ns) -74: Performance: 98.470 0.244 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 17 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 186.7 -74: (ns/day) (hour/ns) -74: Performance: 876.080 0.027 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (62 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.072 0.036 199.3 -74: (ns/day) (hour/ns) -74: Performance: 40.562 0.592 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 14 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 185.9 -74: (ns/day) (hour/ns) -74: Performance: 728.289 0.033 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (100 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.039 0.020 199.0 -74: (ns/day) (hour/ns) -74: Performance: 75.137 0.319 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 187.8 -74: (ns/day) (hour/ns) -74: Performance: 854.451 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (97 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.046 0.023 198.9 -74: (ns/day) (hour/ns) -74: Performance: 64.098 0.374 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 25 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 175.1 -74: (ns/day) (hour/ns) -74: Performance: 705.600 0.034 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (77 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.068 0.034 199.4 -74: (ns/day) (hour/ns) -74: Performance: 42.831 0.560 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 185.9 -74: (ns/day) (hour/ns) -74: Performance: 853.386 0.028 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (91 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.060 0.030 199.3 -74: (ns/day) (hour/ns) -74: Performance: 48.480 0.495 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.012 0.006 193.8 -74: (ns/day) (hour/ns) -74: Performance: 242.945 0.099 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (82 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.026 0.013 198.4 -74: (ns/day) (hour/ns) -74: Performance: 113.457 0.212 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 14 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 189.0 -74: (ns/day) (hour/ns) -74: Performance: 742.151 0.032 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (57 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.049 0.025 199.1 -74: (ns/day) (hour/ns) -74: Performance: 59.170 0.406 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 16 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.004 0.002 188.9 -74: (ns/day) (hour/ns) -74: Performance: 676.245 0.035 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (87 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.048 0.024 198.9 -74: (ns/day) (hour/ns) -74: Performance: 60.612 0.396 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 18 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 184.1 -74: (ns/day) (hour/ns) -74: Performance: 792.767 0.030 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (81 ms) -74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: Setting nstcalcenergy (100) equal to nstenergy (4) -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Number of degrees of freedom in T-Coupling group System is 79.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun '30 atom system in water' -74: 16 steps, 0.0 ps. -74: Generated 2485 of the 2485 non-bonded parameter combinations -74: -74: Generated 2485 of the 2485 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'nonanol' -74: -74: turning H bonds into constraints... -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: -74: turning H bonds into constraints... -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.037 0.018 198.9 -74: (ns/day) (hour/ns) -74: Performance: 80.019 0.300 -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -74: -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' -74: -74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -74: -74: NOTE: 17 % of the run time was spent in pair search, -74: you might want to increase nstlist (this has no effect on accuracy) -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.003 0.002 181.7 -74: (ns/day) (hour/ns) -74: Performance: 794.096 0.030 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -74: -74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (114 ms) -74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (6662 ms total) -74: -74: [----------] 2 tests from Angles1/SimpleMdrunTest -74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file angles1.top, line 72]: -74: In moleculetype 'butane' 4 atoms are not bound by a potential or -74: constraint to any other atom in the same moleculetype. Although -74: technically this might not cause issues in a simulation, this often means -74: that the user forgot to add a bond/potential/constraint or put multiple -74: molecules in the same moleculetype definition by mistake. Run with -v to -74: get information for each atom. -74: -74: Number of degrees of freedom in T-Coupling group System is 9.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: -74: NVE simulation: will use the initial temperature of 238.919 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'This_incredible_box_of_butane' -74: 50 steps, 0.1 ps. -74: Generated 3 of the 3 non-bonded parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'butane' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/angles1.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.027 0.014 198.8 -74: (ns/day) (hour/ns) -74: Performance: 319.240 0.075 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 -74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (23 ms) -74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file angles1.top, line 72]: -74: In moleculetype 'butane' 4 atoms are not bound by a potential or -74: constraint to any other atom in the same moleculetype. Although -74: technically this might not cause issues in a simulation, this often means -74: that the user forgot to add a bond/potential/constraint or put multiple -74: molecules in the same moleculetype definition by mistake. Run with -v to -74: get information for each atom. -74: -74: Number of degrees of freedom in T-Coupling group System is 9.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: -74: NVE simulation: will use the initial temperature of 238.919 K for -74: determining the Verlet buffer size -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -74: Can not increase nstlist because an NVE ensemble is used -74: Using 1 MPI thread -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: starting mdrun 'This_incredible_box_of_butane' -74: 50 steps, 0.1 ps. -74: Generated 3 of the 3 non-bonded parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'butane' -74: -74: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/angles1.gro' -74: -74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K -74: -74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm -74: -74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm -74: -74: Note that mdrun will redetermine rlist based on the actual pair-list setup -74: -74: This run will generate roughly 0 Mb of data -74: -74: Writing final coordinates. -74: -74: Core t (s) Wall t (s) (%) -74: Time: 0.082 0.041 199.7 -74: (ns/day) (hour/ns) -74: Performance: 107.137 0.224 -74: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 -74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (53 ms) -74: [----------] 2 tests from Angles1/SimpleMdrunTest (77 ms total) -74: -74: [----------] Global test environment tear-down -74: [==========] 53 tests from 5 test suites ran. (10187 ms total) -74: [ PASSED ] 53 tests. -74/92 Test #74: MdrunNonIntegratorTests ................... Passed 10.21 sec -test 75 - Start 75: MdrunTpiTests - -75: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" -75: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -75: Test timeout computed to be: 600 -75: [==========] Running 3 tests from 1 test suite. -75: [----------] Global test environment set-up. -75: [----------] 3 tests from Simple/TpiTest -75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (619 ms) -75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (395 ms) -75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 -75: Generating 1-4 interactions: fudge = 0.5 -75: Number of degrees of freedom in T-Coupling group System is 1308.00 -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -75: TPI is not implemented for GPUs. -75: -75: Using 1 MPI thread -75: Using 1 OpenMP thread -75: -75: -75: NOTE: Thread affinity was not set. -75: Reading frames from gro file '216 water molecules', 648 atoms. -75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 -75: Last frame 0 time 0.000 -75: Generated 331705 of the 331705 non-bonded parameter combinations -75: -75: Generated 331705 of the 331705 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: -75: Excluding 3 bonded neighbours molecule type 'methane' -75: Analysing residue names: -75: There are: 216 Water residues -75: There are: 1 Other residues -75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (2991 ms) -75: [----------] 3 tests from Simple/TpiTest (4006 ms total) -75: -75: [----------] Global test environment tear-down -75: [==========] 3 tests from 1 test suite ran. (4089 ms total) -75: [ PASSED ] 3 tests. -75/92 Test #75: MdrunTpiTests ............................. Passed 4.13 sec -test 76 - Start 76: MdrunMpiTests - -76: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" -76: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -76: Test timeout computed to be: 600 -76: [==========] Running 16 tests from 2 test suites. -76: [----------] Global test environment set-up. -76: [----------] 4 tests from MimicTest -76: [ RUN ] MimicTest.OneQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 94 % of the run time was spent in domain decomposition, -76: 0 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.241 0.060 399.7 -76: (ns/day) (hour/ns) -76: Performance: 1.431 16.771 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -302317697 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.OneQuantumMol (156 ms) -76: [ RUN ] MimicTest.AllQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 16 % of the run time was spent in domain decomposition, -76: 15 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 384.5 -76: (ns/day) (hour/ns) -76: Performance: 153.880 0.156 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -2277720 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.AllQuantumMol (52 ms) -76: [ RUN ] MimicTest.TwoQuantumMol -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 21.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -76: -76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 39 % of the run time was spent in domain decomposition, -76: 7 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.172 0.043 399.5 -76: (ns/day) (hour/ns) -76: Performance: 2.007 11.961 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -48333187 -76: -76: Generated 10 of the 10 non-bonded parameter combinations -76: -76: Generated 10 of the 10 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.TwoQuantumMol (174 ms) -76: [ RUN ] MimicTest.BondCuts -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: For a correct single-point energy evaluation with nsteps = 0, use -76: continuation = yes to avoid constraining the input coordinates. -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 66.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: NVE simulation: will use the initial temperature of 300.368 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -76: -76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -76: Reading frame 0 time 0.000 Last frame 0 time 0.000 -76: -76: NOTE: 11 % of the run time was spent in domain decomposition, -76: 9 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.004 0.001 391.8 -76: (ns/day) (hour/ns) -76: Performance: 76.397 0.314 -76: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file -76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -165897 -76: -76: Generated 2211 of the 2211 non-bonded parameter combinations -76: -76: Generated 2211 of the 2211 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: [ OK ] MimicTest.BondCuts (139 ms) -76: [----------] 4 tests from MimicTest (525 ms total) -76: -76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 9.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: There was 1 NOTE -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 9.00 -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group rest is 9.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: NVE simulation with an initial temperature of zero: will use a Verlet -76: buffer of 10%. Check your energy drift! -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: The optimal PME mesh load for parallel simulations is below 0.5 -76: and for highly parallel simulations between 0.25 and 0.33, -76: for higher performance, increase the cut-off and the PME grid spacing. -76: -76: -76: -76: There were 2 NOTEs -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 9.00 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -76: The optimal PME mesh load for parallel simulations is below 0.5 -76: and for highly parallel simulations between 0.25 and 0.33, -76: for higher performance, increase the cut-off and the PME grid spacing. -76: -76: -76: -76: There was 1 NOTE -76: Setting the LD random seed to -756749057 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to -1614992483 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to -1781793987 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -76: Calculating fourier grid dimensions for X Y Z -76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 -76: -76: Estimate for the relative computational load of the PME mesh part: 1.00 -76: -76: This run will generate roughly 0 Mb of data -76: Setting the LD random seed to 2076029934 -76: -76: Generated 3 of the 3 non-bonded parameter combinations -76: -76: Generated 3 of the 3 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -76: -76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -76: -76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: Calculating fourier grid dimensions for X Y Z -76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 -76: -76: Estimate for the relative computational load of the PME mesh part: 1.00 -76: -76: This run will generate roughly 0 Mb of data -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: -76: Dynamic load balancing report: -76: DLB was turned on during the run due to measured imbalance. -76: Average load imbalance: 5.8%. -76: The balanceable part of the MD step is 49%, load imbalance is computed from this. -76: Part of the total run time spent waiting due to load imbalance: 2.8%. -76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -76: -76: -76: NOTE: 42 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.069 0.033 207.8 -76: (ns/day) (hour/ns) -76: Performance: 54.769 0.438 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (93 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: NOTE: 38 % of the run time was spent in domain decomposition, -76: 0 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: NOTE: 26 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.118 0.031 375.9 -76: (ns/day) (hour/ns) -76: Performance: 57.691 0.416 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (165 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot have separate PME ranks when PME is not used -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: -76: Dynamic load balancing report: -76: DLB was off during the run due to low measured imbalance. -76: Average load imbalance: 5.3%. -76: The balanceable part of the MD step is 3%, load imbalance is computed from this. -76: Part of the total run time spent waiting due to load imbalance: 0.1%. -76: -76: -76: NOTE: 13 % of the run time was spent in domain decomposition, -76: 4 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: NOTE: 16 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.245 0.063 388.3 -76: (ns/day) (hour/ns) -76: Performance: 28.706 0.836 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (695 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 1.768 0.442 399.9 -76: (ns/day) (hour/ns) -76: Performance: 4.104 5.847 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (667 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Changing nstlist from 10 to 100, rlist from 1 to 1 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: NOTE: 12 % of the run time was spent communicating energies, -76: you might want to increase some nst* mdp options -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.792 0.200 396.7 -76: (ns/day) (hour/ns) -76: Performance: 9.093 2.639 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (480 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -76: Changing nstlist from 10 to 100, rlist from 1 to 1 -76: -76: Using 2 MPI threads -76: Using 2 OpenMP threads per tMPI thread -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 20 steps, 0.0 ps. -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.801 0.200 399.6 -76: (ns/day) (hour/ns) -76: Performance: 9.057 2.650 -76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (332 ms) -76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped -76: Test configuration is invalid: -76: Cannot use two separate PME ranks when there are less than four ranks total -76: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (2445 ms total) -76: -76: [----------] Global test environment tear-down -76: [==========] 16 tests from 2 test suites ran. (3139 ms total) -76: [ PASSED ] 10 tests. -76: [ SKIPPED ] 6 tests, listed below: -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -76/92 Test #76: MdrunMpiTests ............................. Passed 3.17 sec -test 77 - Start 77: MdrunMultiSimTests - -77: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" -77: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -77: Test timeout computed to be: 600 -77: [==========] Running 2 tests from 1 test suite. -77: [----------] Global test environment set-up. -77: [----------] 2 tests from InNvt/MultiSimTerminationTest -77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) -77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 -77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) -77: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) -77: -77: [----------] Global test environment tear-down -77: [==========] 2 tests from 1 test suite ran. (71 ms total) -77: [ PASSED ] 2 tests. -77: -77: YOU HAVE 4 DISABLED TESTS -77: -77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.11 sec -test 78 - Start 78: MdrunMultiSimReplexTests - -78: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" -78: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -78: Test timeout computed to be: 600 -78: [==========] Running 1 test from 1 test suite. -78: [----------] Global test environment set-up. -78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest -78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) -78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) -78: -78: [----------] Global test environment tear-down -78: [==========] 1 test from 1 test suite ran. (46 ms total) -78: [ PASSED ] 1 test. -78: -78: YOU HAVE 4 DISABLED TESTS -78: -78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.09 sec -test 79 - Start 79: MdrunMultiSimReplexEquivalenceTests - -79: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" -79: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -79: Test timeout computed to be: 600 -79: [==========] Running 0 tests from 0 test suites. -79: [==========] 0 tests from 0 test suites ran. (0 ms total) -79: [ PASSED ] 0 tests. -79: -79: YOU HAVE 10 DISABLED TESTS -79: -79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec -test 80 - Start 80: MdrunMpi1RankPmeTests - -80: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" -80: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -80: Test timeout computed to be: 600 -80: [==========] Running 19 tests from 1 test suite. -80: [----------] Global test environment set-up. -80: [----------] 19 tests from ReproducesEnergies/PmeTest -80: Number of degrees of freedom in T-Coupling group rest is 12.00 -80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: NVE simulation: will use the initial temperature of 1046.791 K for -80: determining the Verlet buffer size -80: -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: The optimal PME mesh load for parallel simulations is below 0.5 -80: and for highly parallel simulations between 0.25 and 0.33, -80: for higher performance, increase the cut-off and the PME grid spacing. -80: -80: -80: -80: There were 2 NOTEs -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: For a correct single-point energy evaluation with nsteps = 0, use -80: continuation = yes to avoid constraining the input coordinates. -80: -80: Number of degrees of freedom in T-Coupling group rest is 13.00 -80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: NVE simulation: will use the initial temperature of 966.268 K for -80: determining the Verlet buffer size -80: -80: -80: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -80: The optimal PME mesh load for parallel simulations is below 0.5 -80: and for highly parallel simulations between 0.25 and 0.33, -80: for higher performance, increase the cut-off and the PME grid spacing. -80: -80: -80: -80: There were 3 NOTEs -80: Setting the LD random seed to 1960639375 -80: -80: Generated 8 of the 10 non-bonded parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'Methanol' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -80: -80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -80: -80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Calculating fourier grid dimensions for X Y Z -80: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 -80: -80: Estimate for the relative computational load of the PME mesh part: 1.00 -80: -80: This run will generate roughly 0 Mb of data -80: Setting the LD random seed to 2143935807 -80: -80: Generated 8 of the 10 non-bonded parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'Methanol' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -80: -80: Searching the wall atom type(s) -80: -80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -80: -80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Calculating fourier grid dimensions for X Y Z -80: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 -80: -80: Estimate for the relative computational load of the PME mesh part: 1.00 -80: -80: This run will generate roughly 0 Mb of data -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.122 0.061 199.6 -80: (ns/day) (hour/ns) -80: Performance: 29.643 0.810 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (258 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.070 0.035 199.4 -80: (ns/day) (hour/ns) -80: Performance: 51.697 0.464 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (89 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 0 steps, 0.0 ps. -80: -80: NOTE: 33 % of the run time was spent in domain decomposition, -80: 11 % of the run time was spent in pair search, -80: you might want to increase nstlist (this has no effect on accuracy) -80: -80: Core t (s) Wall t (s) (%) -80: Time: 0.324 0.162 199.8 -80: (ns/day) (hour/ns) -80: Performance: 0.534 44.977 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file -80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (824 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets using PME rank(s) but the simulation is using only one rank -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -80: Can not increase nstlist because an NVE ensemble is used -80: Using 1 MPI thread -80: Using 2 OpenMP threads -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc-and-methanol' -80: 20 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Core t (s) Wall t (s) (%) -80: Time: 3.570 1.785 200.0 -80: (ns/day) (hour/ns) -80: Performance: 1.017 23.610 -80: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file -80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (1912 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -80: Test is being skipped because: -80: it targets GPU execution, but no compatible devices were detected -80: PME GPU does not support: -80: Double-precision build of GROMACS. -80: Non-GPU build of GROMACS. -80: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -80: [----------] 19 tests from ReproducesEnergies/PmeTest (3089 ms total) -80: -80: [----------] Global test environment tear-down -80: [==========] 19 tests from 1 test suite ran. (3166 ms total) -80: [ PASSED ] 4 tests. -80: [ SKIPPED ] 15 tests, listed below: -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 3.19 sec -test 81 - Start 81: MdrunMpi2RankPmeTests - -81: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" -81: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -81: Test timeout computed to be: 600 -81: [==========] Running 19 tests from 1 test suite. -81: [----------] Global test environment set-up. -81: [----------] 19 tests from ReproducesEnergies/PmeTest -81: Number of degrees of freedom in T-Coupling group rest is 12.00 -81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: NVE simulation: will use the initial temperature of 1046.791 K for -81: determining the Verlet buffer size -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: The optimal PME mesh load for parallel simulations is below 0.5 -81: and for highly parallel simulations between 0.25 and 0.33, -81: for higher performance, increase the cut-off and the PME grid spacing. -81: -81: -81: -81: There were 2 NOTEs -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: For a correct single-point energy evaluation with nsteps = 0, use -81: continuation = yes to avoid constraining the input coordinates. -81: -81: Number of degrees of freedom in T-Coupling group rest is 13.00 -81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: NVE simulation: will use the initial temperature of 966.268 K for -81: determining the Verlet buffer size -81: -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -81: The optimal PME mesh load for parallel simulations is below 0.5 -81: and for highly parallel simulations between 0.25 and 0.33, -81: for higher performance, increase the cut-off and the PME grid spacing. -81: -81: -81: -81: There were 3 NOTEs -81: Setting the LD random seed to -1141899270 -81: -81: Generated 8 of the 10 non-bonded parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'Methanol' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -81: -81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -81: -81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: Calculating fourier grid dimensions for X Y Z -81: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 -81: -81: Estimate for the relative computational load of the PME mesh part: 1.00 -81: -81: This run will generate roughly 0 Mb of data -81: Setting the LD random seed to 2147143519 -81: -81: Generated 8 of the 10 non-bonded parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'Methanol' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -81: -81: Searching the wall atom type(s) -81: -81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -81: -81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: Calculating fourier grid dimensions for X Y Z -81: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 -81: -81: Estimate for the relative computational load of the PME mesh part: 1.00 -81: -81: This run will generate roughly 0 Mb of data -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 12.2%. -81: The balanceable part of the MD step is 5%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.6%. -81: -81: -81: NOTE: 32 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.224 0.056 399.0 -81: (ns/day) (hour/ns) -81: Performance: 32.258 0.744 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (491 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 3.8%. -81: The balanceable part of the MD step is 3%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.1%. -81: -81: -81: NOTE: 30 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.496 0.140 354.5 -81: (ns/day) (hour/ns) -81: Performance: 12.967 1.851 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (483 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 0 steps, 0.0 ps. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.009 0.002 375.3 -81: (ns/day) (hour/ns) -81: Performance: 35.027 0.685 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (612 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 1.576 0.394 399.8 -81: (ns/day) (hour/ns) -81: Performance: 4.602 5.215 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (728 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Core t (s) Wall t (s) (%) -81: Time: 1.323 0.331 399.8 -81: (ns/day) (hour/ns) -81: Performance: 5.481 4.379 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (422 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 0 steps, 0.0 ps. -81: -81: NOTE: 2 % of the run time was spent in domain decomposition, -81: 13 % of the run time was spent in pair search, -81: you might want to increase nstlist (this has no effect on accuracy) -81: -81: Core t (s) Wall t (s) (%) -81: Time: 0.292 0.074 394.4 -81: (ns/day) (hour/ns) -81: Performance: 1.166 20.581 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (814 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -81: Can not increase nstlist because an NVE ensemble is used -81: Using 2 MPI threads -81: Using 2 OpenMP threads per tMPI thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc-and-methanol' -81: 20 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was turned on during the run due to measured imbalance. -81: Average load imbalance: 35.0%. -81: The balanceable part of the MD step is 9%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 3.2%. -81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -81: -81: -81: NOTE: 15 % of the run time was spent in domain decomposition, -81: 0 % of the run time was spent in pair search, -81: you might want to increase nstlist (this has no effect on accuracy) -81: -81: NOTE: 8 % of the run time was spent communicating energies, -81: you might want to increase some nst* mdp options -81: -81: Core t (s) Wall t (s) (%) -81: Time: 1.377 0.344 399.9 -81: (ns/day) (hour/ns) -81: Performance: 5.268 4.556 -81: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (2112 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -81: Test is being skipped because: -81: it targets GPU execution, but no compatible devices were detected -81: it targets PME decomposition, but that is not supported -81: PME GPU does not support: -81: Double-precision build of GROMACS. -81: Non-GPU build of GROMACS. -81: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -81: [----------] 19 tests from ReproducesEnergies/PmeTest (5672 ms total) -81: -81: [----------] Global test environment tear-down -81: [==========] 19 tests from 1 test suite ran. (5751 ms total) -81: [ PASSED ] 7 tests. -81: [ SKIPPED ] 12 tests, listed below: -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 5.78 sec -test 82 - Start 82: MdrunCoordinationBasicTests1Rank - -82: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" -82: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -82: Test timeout computed to be: 1920 -82: [==========] Running 1 test from 1 test suite. -82: [----------] Global test environment set-up. -82: [----------] 1 test from BasicPropagators/PeriodicActionsTest -82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (1) -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: There were 3 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.028 0.028 99.7 -82: (ns/day) (hour/ns) -82: Performance: 51.838 0.463 -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (1) -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: There were 3 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.022 0.022 99.7 -82: (ns/day) (hour/ns) -82: Performance: 66.427 0.361 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: Setting nstcalcenergy (100) equal to nstenergy (4) -82: -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 4. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 4. -82: -82: -82: There were 5 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.009 0.009 99.3 -82: (ns/day) (hour/ns) -82: Performance: 156.265 0.154 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.013 0.013 99.4 -82: (ns/day) (hour/ns) -82: Performance: 116.444 0.206 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.021 0.021 99.6 -82: (ns/day) (hour/ns) -82: Performance: 71.056 0.338 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -82: that with the Verlet scheme, nstlist has no effect on the accuracy of -82: your simulation. -82: -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -82: setting nstcomm equal to nstcalcenergy for less overhead -82: -82: Number of degrees of freedom in T-Coupling group System is 33.00 -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: NVE simulation: will use the initial temperature of 68.810 K for -82: determining the Verlet buffer size -82: -82: -82: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -82: COM removal frequency is set to (1). -82: Other settings require a global communication frequency of 100. -82: Note that this will require additional global communication steps, -82: which will reduce performance when using multiple ranks. -82: Consider setting nstcomm to a multiple of 100. -82: -82: -82: There were 4 NOTEs -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI thread -82: Using 1 OpenMP thread -82: -82: -82: NOTE: Thread affinity was not set. -82: starting mdrun 'Argon' -82: 16 steps, 0.0 ps. -82: Generated 1 of the 1 non-bonded parameter combinations -82: -82: Excluding 1 bonded neighbours molecule type 'Argon' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -82: -82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -82: -82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: -82: This run will generate roughly 0 Mb of data -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.014 0.014 99.5 -82: (ns/day) (hour/ns) -82: Performance: 101.663 0.236 -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -82: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (191 ms) -82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (191 ms total) -82: -82: [----------] Global test environment tear-down -82: [==========] 1 test from 1 test suite ran. (243 ms total) -82: [ PASSED ] 1 test. -82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.26 sec -test 83 - Start 83: MdrunCoordinationBasicTests2Ranks - -83: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" -83: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -83: Test timeout computed to be: 1920 -83: [==========] Running 1 test from 1 test suite. -83: [----------] Global test environment set-up. -83: [----------] 1 test from BasicPropagators/PeriodicActionsTest -83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (1) -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: There were 3 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 0.1%. -83: The balanceable part of the MD step is 52%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.0%. -83: -83: -83: NOTE: 48 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.057 0.029 199.4 -83: (ns/day) (hour/ns) -83: Performance: 51.078 0.470 -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (1) -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: There were 3 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.5%. -83: The balanceable part of the MD step is 51%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.8%. -83: -83: -83: NOTE: 59 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.071 0.047 149.8 -83: (ns/day) (hour/ns) -83: Performance: 30.976 0.775 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: Setting nstcalcenergy (100) equal to nstenergy (4) -83: -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 4. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 4. -83: -83: -83: There were 5 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.1%. -83: The balanceable part of the MD step is 6%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.1%. -83: -83: -83: NOTE: 32 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.039 0.020 199.2 -83: (ns/day) (hour/ns) -83: Performance: 74.064 0.324 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was turned on during the run due to measured imbalance. -83: Average load imbalance: 10.9%. -83: The balanceable part of the MD step is 40%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 4.3%. -83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -83: -83: -83: NOTE: 47 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.026 0.013 198.6 -83: (ns/day) (hour/ns) -83: Performance: 112.393 0.214 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.2%. -83: The balanceable part of the MD step is 37%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.4%. -83: -83: -83: NOTE: 49 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.072 0.036 199.4 -83: (ns/day) (hour/ns) -83: Performance: 40.541 0.592 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -83: that with the Verlet scheme, nstlist has no effect on the accuracy of -83: your simulation. -83: -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -83: setting nstcomm equal to nstcalcenergy for less overhead -83: -83: Number of degrees of freedom in T-Coupling group System is 33.00 -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: NVE simulation: will use the initial temperature of 68.810 K for -83: determining the Verlet buffer size -83: -83: -83: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -83: COM removal frequency is set to (1). -83: Other settings require a global communication frequency of 100. -83: Note that this will require additional global communication steps, -83: which will reduce performance when using multiple ranks. -83: Consider setting nstcomm to a multiple of 100. -83: -83: -83: There were 4 NOTEs -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI threads -83: Using 1 OpenMP thread per tMPI thread -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'Argon' -83: 16 steps, 0.0 ps. -83: Generated 1 of the 1 non-bonded parameter combinations -83: -83: Excluding 1 bonded neighbours molecule type 'Argon' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -83: -83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -83: -83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: -83: This run will generate roughly 0 Mb of data -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 0.2%. -83: The balanceable part of the MD step is 36%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.1%. -83: -83: -83: NOTE: 48 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.034 0.017 199.1 -83: (ns/day) (hour/ns) -83: Performance: 87.138 0.275 -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -83: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (828 ms) -83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (828 ms total) -83: -83: [----------] Global test environment tear-down -83: [==========] 1 test from 1 test suite ran. (894 ms total) -83: [ PASSED ] 1 test. -83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 0.93 sec -test 84 - Start 84: MdrunCoordinationCouplingTests1Rank - -84: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" -84: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -84: Test timeout computed to be: 1920 -84: [==========] Running 25 tests from 1 test suite. -84: [----------] Global test environment set-up. -84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.5 -84: (ns/day) (hour/ns) -84: Performance: 114.921 0.209 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.4 -84: (ns/day) (hour/ns) -84: Performance: 123.170 0.195 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.3 -84: (ns/day) (hour/ns) -84: Performance: 145.280 0.165 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 109.844 0.218 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.034 0.035 99.8 -84: (ns/day) (hour/ns) -84: Performance: 42.548 0.564 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.5 -84: (ns/day) (hour/ns) -84: Performance: 98.211 0.244 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (204 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.3 -84: (ns/day) (hour/ns) -84: Performance: 125.007 0.192 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 98.9 -84: (ns/day) (hour/ns) -84: Performance: 175.216 0.137 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.1 -84: (ns/day) (hour/ns) -84: Performance: 133.468 0.180 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.017 92.5 -84: (ns/day) (hour/ns) -84: Performance: 85.573 0.280 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 98.3 -84: (ns/day) (hour/ns) -84: Performance: 106.102 0.226 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.0 -84: (ns/day) (hour/ns) -84: Performance: 69.910 0.343 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (202 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.6 -84: (ns/day) (hour/ns) -84: Performance: 76.137 0.315 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.2 -84: (ns/day) (hour/ns) -84: Performance: 176.825 0.136 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.027 0.027 99.6 -84: (ns/day) (hour/ns) -84: Performance: 54.670 0.439 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 115.711 0.207 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.2 -84: (ns/day) (hour/ns) -84: Performance: 99.828 0.240 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.6 -84: (ns/day) (hour/ns) -84: Performance: 80.558 0.298 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (216 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.022 0.022 99.6 -84: (ns/day) (hour/ns) -84: Performance: 66.960 0.358 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.0 -84: (ns/day) (hour/ns) -84: Performance: 100.120 0.240 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.024 0.024 99.3 -84: (ns/day) (hour/ns) -84: Performance: 60.374 0.398 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.0 -84: (ns/day) (hour/ns) -84: Performance: 68.583 0.350 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 102.853 0.233 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.3 -84: (ns/day) (hour/ns) -84: Performance: 122.365 0.196 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (240 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.013 93.6 -84: (ns/day) (hour/ns) -84: Performance: 112.448 0.213 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.017 81.7 -84: (ns/day) (hour/ns) -84: Performance: 85.658 0.280 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.017 99.6 -84: (ns/day) (hour/ns) -84: Performance: 88.982 0.270 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.5 -84: (ns/day) (hour/ns) -84: Performance: 115.896 0.207 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.6 -84: (ns/day) (hour/ns) -84: Performance: 81.288 0.295 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 114.180 0.210 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (207 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.6 -84: (ns/day) (hour/ns) -84: Performance: 77.445 0.310 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.3 -84: (ns/day) (hour/ns) -84: Performance: 137.012 0.175 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.010 69.2 -84: (ns/day) (hour/ns) -84: Performance: 147.584 0.163 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.2 -84: (ns/day) (hour/ns) -84: Performance: 70.265 0.342 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.4 -84: (ns/day) (hour/ns) -84: Performance: 80.301 0.299 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.2 -84: (ns/day) (hour/ns) -84: Performance: 149.707 0.160 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (200 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.034 0.034 99.8 -84: (ns/day) (hour/ns) -84: Performance: 43.341 0.554 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.023 0.023 99.7 -84: (ns/day) (hour/ns) -84: Performance: 64.532 0.372 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.6 -84: (ns/day) (hour/ns) -84: Performance: 77.318 0.310 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.026 0.026 99.2 -84: (ns/day) (hour/ns) -84: Performance: 56.674 0.423 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.034 0.039 88.3 -84: (ns/day) (hour/ns) -84: Performance: 37.950 0.632 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.037 0.038 99.1 -84: (ns/day) (hour/ns) -84: Performance: 38.819 0.618 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (352 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.111 0.111 99.9 -84: (ns/day) (hour/ns) -84: Performance: 13.239 1.813 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.033 0.033 99.8 -84: (ns/day) (hour/ns) -84: Performance: 44.898 0.535 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 116.203 0.207 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.068 0.069 99.9 -84: (ns/day) (hour/ns) -84: Performance: 21.422 1.120 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.027 0.027 99.6 -84: (ns/day) (hour/ns) -84: Performance: 54.148 0.443 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.5 -84: (ns/day) (hour/ns) -84: Performance: 97.342 0.247 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (378 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 107.027 0.224 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.3 -84: (ns/day) (hour/ns) -84: Performance: 90.676 0.265 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.043 0.043 99.8 -84: (ns/day) (hour/ns) -84: Performance: 33.791 0.710 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.5 -84: (ns/day) (hour/ns) -84: Performance: 76.740 0.313 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 103.321 0.232 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 95.9 -84: (ns/day) (hour/ns) -84: Performance: 75.461 0.318 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (245 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.5 -84: (ns/day) (hour/ns) -84: Performance: 85.658 0.280 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.014 88.8 -84: (ns/day) (hour/ns) -84: Performance: 107.543 0.223 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.7 -84: (ns/day) (hour/ns) -84: Performance: 68.427 0.351 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.014 99.4 -84: (ns/day) (hour/ns) -84: Performance: 108.347 0.222 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.012 99.2 -84: (ns/day) (hour/ns) -84: Performance: 127.332 0.188 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.5 -84: (ns/day) (hour/ns) -84: Performance: 91.279 0.263 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (214 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.3 -84: (ns/day) (hour/ns) -84: Performance: 103.060 0.233 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.5 -84: (ns/day) (hour/ns) -84: Performance: 85.183 0.282 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.5 -84: (ns/day) (hour/ns) -84: Performance: 82.614 0.291 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.4 -84: (ns/day) (hour/ns) -84: Performance: 103.646 0.232 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 95.0 -84: (ns/day) (hour/ns) -84: Performance: 84.302 0.285 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.024 0.024 99.4 -84: (ns/day) (hour/ns) -84: Performance: 61.711 0.389 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (296 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.3 -84: (ns/day) (hour/ns) -84: Performance: 138.046 0.174 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.023 0.023 99.7 -84: (ns/day) (hour/ns) -84: Performance: 64.978 0.369 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 98.4 -84: (ns/day) (hour/ns) -84: Performance: 163.663 0.147 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.5 -84: (ns/day) (hour/ns) -84: Performance: 96.264 0.249 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.3 -84: (ns/day) (hour/ns) -84: Performance: 126.832 0.189 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -84: 1 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.042 0.042 99.8 -84: (ns/day) (hour/ns) -84: Performance: 35.273 0.680 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (218 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.037 0.037 99.8 -84: (ns/day) (hour/ns) -84: Performance: 39.336 0.610 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 98.0 -84: (ns/day) (hour/ns) -84: Performance: 150.435 0.160 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.5 -84: (ns/day) (hour/ns) -84: Performance: 113.961 0.211 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.011 99.4 -84: (ns/day) (hour/ns) -84: Performance: 139.018 0.173 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.5 -84: (ns/day) (hour/ns) -84: Performance: 108.860 0.220 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.042 0.042 99.8 -84: (ns/day) (hour/ns) -84: Performance: 34.639 0.693 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (225 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.4 -84: (ns/day) (hour/ns) -84: Performance: 122.665 0.196 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.4 -84: (ns/day) (hour/ns) -84: Performance: 125.053 0.192 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.5 -84: (ns/day) (hour/ns) -84: Performance: 121.539 0.197 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.5 -84: (ns/day) (hour/ns) -84: Performance: 119.082 0.202 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.4 -84: (ns/day) (hour/ns) -84: Performance: 127.726 0.188 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 112.356 0.214 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (139 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.3 -84: (ns/day) (hour/ns) -84: Performance: 134.543 0.178 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 98.8 -84: (ns/day) (hour/ns) -84: Performance: 218.020 0.110 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.1 -84: (ns/day) (hour/ns) -84: Performance: 194.059 0.124 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.3 -84: (ns/day) (hour/ns) -84: Performance: 142.432 0.169 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.3 -84: (ns/day) (hour/ns) -84: Performance: 134.876 0.178 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.016 99.3 -84: (ns/day) (hour/ns) -84: Performance: 94.315 0.254 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (130 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.4 -84: (ns/day) (hour/ns) -84: Performance: 125.509 0.191 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.1 -84: (ns/day) (hour/ns) -84: Performance: 162.287 0.148 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.2 -84: (ns/day) (hour/ns) -84: Performance: 181.247 0.132 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.2 -84: (ns/day) (hour/ns) -84: Performance: 147.221 0.163 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 104.048 0.231 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.3 -84: (ns/day) (hour/ns) -84: Performance: 144.914 0.166 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (121 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.7 -84: (ns/day) (hour/ns) -84: Performance: 89.663 0.268 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.6 -84: (ns/day) (hour/ns) -84: Performance: 128.036 0.187 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.023 0.023 99.8 -84: (ns/day) (hour/ns) -84: Performance: 64.389 0.373 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.020 0.020 99.8 -84: (ns/day) (hour/ns) -84: Performance: 72.673 0.330 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.022 0.022 99.6 -84: (ns/day) (hour/ns) -84: Performance: 67.987 0.353 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.7 -84: (ns/day) (hour/ns) -84: Performance: 86.904 0.276 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (175 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.6 -84: (ns/day) (hour/ns) -84: Performance: 117.513 0.204 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.6 -84: (ns/day) (hour/ns) -84: Performance: 98.991 0.242 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.022 0.022 99.8 -84: (ns/day) (hour/ns) -84: Performance: 67.655 0.355 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.6 -84: (ns/day) (hour/ns) -84: Performance: 95.651 0.251 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.7 -84: (ns/day) (hour/ns) -84: Performance: 78.839 0.304 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.7 -84: (ns/day) (hour/ns) -84: Performance: 77.697 0.309 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (159 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.039 0.039 99.8 -84: (ns/day) (hour/ns) -84: Performance: 37.647 0.638 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 107.829 0.223 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.6 -84: (ns/day) (hour/ns) -84: Performance: 122.692 0.196 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.155 0.155 100.0 -84: (ns/day) (hour/ns) -84: Performance: 9.497 2.527 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.019 0.019 99.7 -84: (ns/day) (hour/ns) -84: Performance: 77.710 0.309 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.7 -84: (ns/day) (hour/ns) -84: Performance: 91.822 0.261 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (309 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.042 0.042 99.8 -84: (ns/day) (hour/ns) -84: Performance: 35.210 0.682 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.035 0.035 99.8 -84: (ns/day) (hour/ns) -84: Performance: 41.810 0.574 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.022 0.022 99.8 -84: (ns/day) (hour/ns) -84: Performance: 65.720 0.365 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.029 0.030 99.8 -84: (ns/day) (hour/ns) -84: Performance: 49.782 0.482 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.026 0.026 99.7 -84: (ns/day) (hour/ns) -84: Performance: 57.264 0.419 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.7 -84: (ns/day) (hour/ns) -84: Performance: 80.278 0.299 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (236 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.6 -84: (ns/day) (hour/ns) -84: Performance: 91.305 0.263 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.4 -84: (ns/day) (hour/ns) -84: Performance: 112.313 0.214 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.5 -84: (ns/day) (hour/ns) -84: Performance: 125.190 0.192 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.022 0.022 99.7 -84: (ns/day) (hour/ns) -84: Performance: 67.955 0.353 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.014 0.014 99.5 -84: (ns/day) (hour/ns) -84: Performance: 107.227 0.224 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -84: The Berendsen barostat does not generate any strictly correct ensemble, -84: and should not be used for new production simulations (in our opinion). -84: We recommend using the C-rescale barostat instead. -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: -84: There was 1 WARNING -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.5 -84: (ns/day) (hour/ns) -84: Performance: 89.570 0.268 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (140 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.7 -84: (ns/day) (hour/ns) -84: Performance: 69.088 0.347 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.5 -84: (ns/day) (hour/ns) -84: Performance: 132.472 0.181 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 98.8 -84: (ns/day) (hour/ns) -84: Performance: 122.741 0.196 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.021 0.021 99.8 -84: (ns/day) (hour/ns) -84: Performance: 69.201 0.347 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.8 -84: (ns/day) (hour/ns) -84: Performance: 84.757 0.283 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.7 -84: (ns/day) (hour/ns) -84: Performance: 124.118 0.193 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (141 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.7 -84: (ns/day) (hour/ns) -84: Performance: 112.668 0.213 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.7 -84: (ns/day) (hour/ns) -84: Performance: 115.722 0.207 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.5 -84: (ns/day) (hour/ns) -84: Performance: 138.186 0.174 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.5 -84: (ns/day) (hour/ns) -84: Performance: 123.627 0.194 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.6 -84: (ns/day) (hour/ns) -84: Performance: 91.916 0.261 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.020 0.020 99.7 -84: (ns/day) (hour/ns) -84: Performance: 74.626 0.322 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (594 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.027 0.027 99.7 -84: (ns/day) (hour/ns) -84: Performance: 54.297 0.442 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.015 0.015 99.5 -84: (ns/day) (hour/ns) -84: Performance: 97.893 0.245 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.5 -84: (ns/day) (hour/ns) -84: Performance: 87.444 0.274 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.018 0.018 99.6 -84: (ns/day) (hour/ns) -84: Performance: 80.518 0.298 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.013 0.013 99.5 -84: (ns/day) (hour/ns) -84: Performance: 111.550 0.215 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: MTTK coupling is deprecated and will soon be removed -84: -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: for current Trotter decomposition methods with vv, nsttcouple and -84: nstpcouple must be equal. Both have been reset to -84: min(nsttcouple,nstpcouple) = 2 -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -84: COM removal frequency is set to (5). -84: Other settings require a global communication frequency of 2. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 2. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.017 0.017 99.6 -84: (ns/day) (hour/ns) -84: Performance: 87.455 0.274 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (154 ms) -84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.6 -84: (ns/day) (hour/ns) -84: Performance: 121.176 0.198 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.010 0.010 99.4 -84: (ns/day) (hour/ns) -84: Performance: 140.833 0.170 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.011 0.011 99.3 -84: (ns/day) (hour/ns) -84: Performance: 136.299 0.176 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.3 -84: (ns/day) (hour/ns) -84: Performance: 123.898 0.194 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.012 0.012 99.5 -84: (ns/day) (hour/ns) -84: Performance: 117.665 0.204 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: There were 2 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -84: -84: Using 1 MPI thread -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.016 0.016 99.6 -84: (ns/day) (hour/ns) -84: Performance: 91.871 0.261 -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (115 ms) -84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (5622 ms total) -84: -84: [----------] Global test environment tear-down -84: [==========] 25 tests from 1 test suite ran. (5679 ms total) -84: [ PASSED ] 25 tests. -84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 5.72 sec -test 85 - Start 85: MdrunCoordinationCouplingTests2Ranks - -85: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" -85: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -85: Test timeout computed to be: 1920 -85: [==========] Running 25 tests from 1 test suite. -85: [----------] Global test environment set-up. -85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.7%. -85: The balanceable part of the MD step is 54%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.9%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.8 -85: (ns/day) (hour/ns) -85: Performance: 120.147 0.200 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.3%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.7%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 184.936 0.130 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.2%. -85: The balanceable part of the MD step is 39%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.4%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.4 -85: (ns/day) (hour/ns) -85: Performance: 170.715 0.141 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 7.9%. -85: The balanceable part of the MD step is 38%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 3.0%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 144.106 0.167 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 4.5%. -85: The balanceable part of the MD step is 39%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.8%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.026 0.013 198.5 -85: (ns/day) (hour/ns) -85: Performance: 111.777 0.215 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 5.5%. -85: The balanceable part of the MD step is 39%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.1%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.6 -85: (ns/day) (hour/ns) -85: Performance: 134.718 0.178 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (126 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.4%. -85: The balanceable part of the MD step is 56%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.9%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.7 -85: (ns/day) (hour/ns) -85: Performance: 119.230 0.201 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.8%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.5%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 191.856 0.125 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.7%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.4 -85: (ns/day) (hour/ns) -85: Performance: 198.249 0.121 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.2%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.4%. -85: -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 199.1 -85: (ns/day) (hour/ns) -85: Performance: 134.583 0.178 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.4%. -85: The balanceable part of the MD step is 41%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.6%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.2 -85: (ns/day) (hour/ns) -85: Performance: 205.751 0.117 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 5.0%. -85: The balanceable part of the MD step is 46%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.3%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 143.847 0.167 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (107 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.5%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 174.655 0.137 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.1%. -85: The balanceable part of the MD step is 48%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 188.625 0.127 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.7%. -85: The balanceable part of the MD step is 46%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.2%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.1 -85: (ns/day) (hour/ns) -85: Performance: 177.800 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.3%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.6%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.7 -85: (ns/day) (hour/ns) -85: Performance: 178.529 0.134 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.0%. -85: The balanceable part of the MD step is 46%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.4%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.9 -85: (ns/day) (hour/ns) -85: Performance: 139.374 0.172 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.7%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 198.2 -85: (ns/day) (hour/ns) -85: Performance: 155.651 0.154 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (96 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.3%. -85: The balanceable part of the MD step is 53%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.035 0.018 199.2 -85: (ns/day) (hour/ns) -85: Performance: 82.907 0.289 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.2%. -85: The balanceable part of the MD step is 49%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.1%. -85: -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.033 0.017 199.0 -85: (ns/day) (hour/ns) -85: Performance: 88.987 0.270 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 5.9%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.6%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.5 -85: (ns/day) (hour/ns) -85: Performance: 203.293 0.118 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.3%. -85: The balanceable part of the MD step is 43%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.4%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.4 -85: (ns/day) (hour/ns) -85: Performance: 187.511 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.8%. -85: The balanceable part of the MD step is 39%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.7%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.7 -85: (ns/day) (hour/ns) -85: Performance: 138.909 0.173 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.2%. -85: The balanceable part of the MD step is 41%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.035 0.018 199.2 -85: (ns/day) (hour/ns) -85: Performance: 83.548 0.287 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (126 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.042 0.021 199.4 -85: (ns/day) (hour/ns) -85: Performance: 69.917 0.343 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 203.781 0.118 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.5 -85: (ns/day) (hour/ns) -85: Performance: 212.189 0.113 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 140.044 0.171 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 149.885 0.160 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.011 199.1 -85: (ns/day) (hour/ns) -85: Performance: 129.150 0.186 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (106 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 190.001 0.126 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.006 198.3 -85: (ns/day) (hour/ns) -85: Performance: 256.852 0.093 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.025 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 117.560 0.204 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 50 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.191 0.096 199.8 -85: (ns/day) (hour/ns) -85: Performance: 15.353 1.563 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.9 -85: (ns/day) (hour/ns) -85: Performance: 158.660 0.151 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 50 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.145 0.073 199.8 -85: (ns/day) (hour/ns) -85: Performance: 20.190 1.189 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (291 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 199.0 -85: (ns/day) (hour/ns) -85: Performance: 152.174 0.158 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.7 -85: (ns/day) (hour/ns) -85: Performance: 186.273 0.129 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.011 183.6 -85: (ns/day) (hour/ns) -85: Performance: 132.406 0.181 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.8 -85: (ns/day) (hour/ns) -85: Performance: 162.669 0.148 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.8 -85: (ns/day) (hour/ns) -85: Performance: 150.348 0.160 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 199.1 -85: (ns/day) (hour/ns) -85: Performance: 130.124 0.184 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (101 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.9 -85: (ns/day) (hour/ns) -85: Performance: 160.461 0.150 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.3 -85: (ns/day) (hour/ns) -85: Performance: 207.347 0.116 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.2 -85: (ns/day) (hour/ns) -85: Performance: 201.927 0.119 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.3 -85: (ns/day) (hour/ns) -85: Performance: 159.119 0.151 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.9 -85: (ns/day) (hour/ns) -85: Performance: 127.127 0.189 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 197.9 -85: (ns/day) (hour/ns) -85: Performance: 154.690 0.155 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (95 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.8 -85: (ns/day) (hour/ns) -85: Performance: 169.922 0.141 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.8 -85: (ns/day) (hour/ns) -85: Performance: 193.292 0.124 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.2 -85: (ns/day) (hour/ns) -85: Performance: 215.165 0.112 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.9 -85: (ns/day) (hour/ns) -85: Performance: 152.685 0.157 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 199.3 -85: (ns/day) (hour/ns) -85: Performance: 131.911 0.182 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 199.3 -85: (ns/day) (hour/ns) -85: Performance: 132.292 0.181 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (98 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 199.2 -85: (ns/day) (hour/ns) -85: Performance: 127.459 0.188 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 174.321 0.138 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 195.860 0.123 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 199.1 -85: (ns/day) (hour/ns) -85: Performance: 152.796 0.157 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 199.1 -85: (ns/day) (hour/ns) -85: Performance: 156.218 0.154 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.027 0.013 199.3 -85: (ns/day) (hour/ns) -85: Performance: 110.341 0.218 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (111 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.027 0.014 199.3 -85: (ns/day) (hour/ns) -85: Performance: 107.596 0.223 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.9 -85: (ns/day) (hour/ns) -85: Performance: 143.701 0.167 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.007 198.9 -85: (ns/day) (hour/ns) -85: Performance: 197.540 0.121 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 199.0 -85: (ns/day) (hour/ns) -85: Performance: 160.696 0.149 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 199.2 -85: (ns/day) (hour/ns) -85: Performance: 124.072 0.193 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 199.1 -85: (ns/day) (hour/ns) -85: Performance: 131.673 0.182 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (105 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 43 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 198.9 -85: (ns/day) (hour/ns) -85: Performance: 156.440 0.153 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.3 -85: (ns/day) (hour/ns) -85: Performance: 222.980 0.108 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.7 -85: (ns/day) (hour/ns) -85: Performance: 178.049 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.9 -85: (ns/day) (hour/ns) -85: Performance: 158.274 0.152 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.8 -85: (ns/day) (hour/ns) -85: Performance: 170.041 0.141 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -85: 1 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 198.8 -85: (ns/day) (hour/ns) -85: Performance: 156.966 0.153 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (90 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 199.0 -85: (ns/day) (hour/ns) -85: Performance: 149.400 0.161 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 199.1 -85: (ns/day) (hour/ns) -85: Performance: 166.647 0.144 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 226.859 0.106 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 199.2 -85: (ns/day) (hour/ns) -85: Performance: 126.905 0.189 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 123.378 0.195 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.034 0.017 199.6 -85: (ns/day) (hour/ns) -85: Performance: 86.171 0.279 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (114 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 199.3 -85: (ns/day) (hour/ns) -85: Performance: 122.421 0.196 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 199.1 -85: (ns/day) (hour/ns) -85: Performance: 169.335 0.142 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 251.494 0.095 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 48 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 199.0 -85: (ns/day) (hour/ns) -85: Performance: 185.652 0.129 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.6 -85: (ns/day) (hour/ns) -85: Performance: 253.069 0.095 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 218.600 0.110 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (87 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 208.873 0.115 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.011 0.005 198.5 -85: (ns/day) (hour/ns) -85: Performance: 268.120 0.090 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.008 0.004 198.1 -85: (ns/day) (hour/ns) -85: Performance: 343.553 0.070 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.8 -85: (ns/day) (hour/ns) -85: Performance: 220.143 0.109 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.7 -85: (ns/day) (hour/ns) -85: Performance: 235.912 0.102 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 198.9 -85: (ns/day) (hour/ns) -85: Performance: 195.385 0.123 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (65 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.8 -85: (ns/day) (hour/ns) -85: Performance: 151.956 0.158 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.009 0.005 198.2 -85: (ns/day) (hour/ns) -85: Performance: 307.469 0.078 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.009 0.004 197.9 -85: (ns/day) (hour/ns) -85: Performance: 327.213 0.073 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.6 -85: (ns/day) (hour/ns) -85: Performance: 215.741 0.111 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 198.7 -85: (ns/day) (hour/ns) -85: Performance: 211.504 0.113 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.4 -85: (ns/day) (hour/ns) -85: Performance: 250.034 0.096 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (67 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.6%. -85: The balanceable part of the MD step is 62%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.0%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.022 0.011 198.4 -85: (ns/day) (hour/ns) -85: Performance: 132.213 0.182 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.4%. -85: The balanceable part of the MD step is 57%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.0%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 197.6 -85: (ns/day) (hour/ns) -85: Performance: 223.838 0.107 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.6%. -85: The balanceable part of the MD step is 50%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 197.6 -85: (ns/day) (hour/ns) -85: Performance: 220.348 0.109 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.7%. -85: The balanceable part of the MD step is 44%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.1%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.9 -85: (ns/day) (hour/ns) -85: Performance: 177.396 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.8%. -85: The balanceable part of the MD step is 47%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.0 -85: (ns/day) (hour/ns) -85: Performance: 146.109 0.164 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.0%. -85: The balanceable part of the MD step is 48%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.9%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.008 197.7 -85: (ns/day) (hour/ns) -85: Performance: 175.331 0.137 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (80 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.4%. -85: The balanceable part of the MD step is 58%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.012 198.1 -85: (ns/day) (hour/ns) -85: Performance: 127.028 0.189 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.4%. -85: The balanceable part of the MD step is 58%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.6 -85: (ns/day) (hour/ns) -85: Performance: 177.633 0.135 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.5%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 196.6 -85: (ns/day) (hour/ns) -85: Performance: 210.900 0.114 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.6%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 197.7 -85: (ns/day) (hour/ns) -85: Performance: 152.456 0.157 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 2.8%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.4%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.9 -85: (ns/day) (hour/ns) -85: Performance: 163.106 0.147 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.0%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.5%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.7 -85: (ns/day) (hour/ns) -85: Performance: 178.534 0.134 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (83 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.4%. -85: The balanceable part of the MD step is 59%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 142.944 0.168 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.3%. -85: The balanceable part of the MD step is 59%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.8%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 198.0 -85: (ns/day) (hour/ns) -85: Performance: 176.317 0.136 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 1.7%. -85: The balanceable part of the MD step is 54%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.9%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.9 -85: (ns/day) (hour/ns) -85: Performance: 185.801 0.129 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 6.2%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 3.2%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.023 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 128.904 0.186 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was turned on during the run due to measured imbalance. -85: Average load imbalance: 4.4%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 2.2%. -85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.9 -85: (ns/day) (hour/ns) -85: Performance: 163.606 0.147 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 3.1%. -85: The balanceable part of the MD step is 52%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 1.6%. -85: -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.6 -85: (ns/day) (hour/ns) -85: Performance: 122.098 0.197 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (90 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.5 -85: (ns/day) (hour/ns) -85: Performance: 138.694 0.173 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 154.558 0.155 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 197.8 -85: (ns/day) (hour/ns) -85: Performance: 192.236 0.125 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.3 -85: (ns/day) (hour/ns) -85: Performance: 137.033 0.175 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.027 0.013 198.6 -85: (ns/day) (hour/ns) -85: Performance: 109.629 0.219 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.026 0.013 198.3 -85: (ns/day) (hour/ns) -85: Performance: 113.868 0.211 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (107 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.025 0.013 198.7 -85: (ns/day) (hour/ns) -85: Performance: 116.912 0.205 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.021 0.011 198.2 -85: (ns/day) (hour/ns) -85: Performance: 138.633 0.173 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 197.2 -85: (ns/day) (hour/ns) -85: Performance: 231.889 0.103 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.9 -85: (ns/day) (hour/ns) -85: Performance: 176.397 0.136 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.9 -85: (ns/day) (hour/ns) -85: Performance: 179.064 0.134 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -85: The Berendsen barostat does not generate any strictly correct ensemble, -85: and should not be used for new production simulations (in our opinion). -85: We recommend using the C-rescale barostat instead. -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: -85: There was 1 WARNING -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.8 -85: (ns/day) (hour/ns) -85: Performance: 184.419 0.130 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (83 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 167.592 0.143 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 197.3 -85: (ns/day) (hour/ns) -85: Performance: 209.288 0.115 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.006 197.3 -85: (ns/day) (hour/ns) -85: Performance: 226.526 0.106 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.8 -85: (ns/day) (hour/ns) -85: Performance: 183.488 0.131 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.1 -85: (ns/day) (hour/ns) -85: Performance: 150.744 0.159 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 145.205 0.165 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (77 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.1 -85: (ns/day) (hour/ns) -85: Performance: 171.425 0.140 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 196.9 -85: (ns/day) (hour/ns) -85: Performance: 224.761 0.107 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.014 0.007 197.2 -85: (ns/day) (hour/ns) -85: Performance: 213.494 0.112 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.8 -85: (ns/day) (hour/ns) -85: Performance: 157.080 0.153 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.016 0.008 197.6 -85: (ns/day) (hour/ns) -85: Performance: 186.795 0.128 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 160.595 0.149 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (75 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.010 198.2 -85: (ns/day) (hour/ns) -85: Performance: 151.465 0.158 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 197.8 -85: (ns/day) (hour/ns) -85: Performance: 168.040 0.143 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.015 0.008 197.5 -85: (ns/day) (hour/ns) -85: Performance: 193.010 0.124 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.7 -85: (ns/day) (hour/ns) -85: Performance: 158.838 0.151 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 197.9 -85: (ns/day) (hour/ns) -85: Performance: 156.233 0.154 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: MTTK coupling is deprecated and will soon be removed -85: -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: for current Trotter decomposition methods with vv, nsttcouple and -85: nstpcouple must be equal. Both have been reset to -85: min(nsttcouple,nstpcouple) = 2 -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -85: COM removal frequency is set to (5). -85: Other settings require a global communication frequency of 2. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 2. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.8 -85: (ns/day) (hour/ns) -85: Performance: 163.022 0.147 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (81 ms) -85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.3 -85: (ns/day) (hour/ns) -85: Performance: 145.949 0.164 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 198.0 -85: (ns/day) (hour/ns) -85: Performance: 162.776 0.147 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 197.3 -85: (ns/day) (hour/ns) -85: Performance: 214.932 0.112 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.019 0.009 197.6 -85: (ns/day) (hour/ns) -85: Performance: 156.442 0.153 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.024 0.012 198.0 -85: (ns/day) (hour/ns) -85: Performance: 120.654 0.199 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: There were 2 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -85: -85: Using 2 MPI threads -85: Using 1 OpenMP thread per tMPI thread -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: Writing final coordinates. -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.018 0.009 197.9 -85: (ns/day) (hour/ns) -85: Performance: 158.388 0.152 -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file -85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (84 ms) -85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (2553 ms total) -85: -85: [----------] Global test environment tear-down -85: [==========] 25 tests from 1 test suite ran. (2589 ms total) -85: [ PASSED ] 25 tests. -85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 2.60 sec -test 86 - Start 86: MdrunCoordinationConstraintsTests1Rank - -86: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" -86: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -86: Test timeout computed to be: 1920 -86: [==========] Running 13 tests from 1 test suite. -86: [----------] Global test environment set-up. -86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 165.203 0.145 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.020 0.020 99.7 -86: (ns/day) (hour/ns) -86: Performance: 71.838 0.334 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 221.732 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 227.068 0.106 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 171.901 0.140 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.5 -86: (ns/day) (hour/ns) -86: Performance: 143.300 0.167 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1731 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.5 -86: (ns/day) (hour/ns) -86: Performance: 97.845 0.245 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.009 99.3 -86: (ns/day) (hour/ns) -86: Performance: 172.040 0.140 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.1 -86: (ns/day) (hour/ns) -86: Performance: 255.552 0.094 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.4 -86: (ns/day) (hour/ns) -86: Performance: 152.524 0.157 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.145 0.145 100.0 -86: (ns/day) (hour/ns) -86: Performance: 10.133 2.368 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.388 0.388 100.0 -86: (ns/day) (hour/ns) -86: Performance: 3.784 6.343 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2940 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.498 0.499 100.0 -86: (ns/day) (hour/ns) -86: Performance: 2.946 8.146 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.343 0.343 100.0 -86: (ns/day) (hour/ns) -86: Performance: 4.279 5.609 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.132 0.132 100.0 -86: (ns/day) (hour/ns) -86: Performance: 11.133 2.156 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.7 -86: (ns/day) (hour/ns) -86: Performance: 97.832 0.245 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 213.746 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 207.190 0.116 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3366 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.012 99.4 -86: (ns/day) (hour/ns) -86: Performance: 127.348 0.188 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.1 -86: (ns/day) (hour/ns) -86: Performance: 227.085 0.106 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 98.9 -86: (ns/day) (hour/ns) -86: Performance: 228.314 0.105 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 182.196 0.132 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.080 0.080 100.0 -86: (ns/day) (hour/ns) -86: Performance: 18.424 1.303 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.083 0.083 99.9 -86: (ns/day) (hour/ns) -86: Performance: 17.654 1.359 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1880 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.440 0.440 100.0 -86: (ns/day) (hour/ns) -86: Performance: 3.340 7.185 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.4 -86: (ns/day) (hour/ns) -86: Performance: 230.950 0.104 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 184.416 0.130 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.4 -86: (ns/day) (hour/ns) -86: Performance: 137.244 0.175 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 200.462 0.120 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 198.986 0.121 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2157 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.056 0.056 99.9 -86: (ns/day) (hour/ns) -86: Performance: 26.149 0.918 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.3 -86: (ns/day) (hour/ns) -86: Performance: 277.592 0.086 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 218.120 0.110 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 166.732 0.144 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.024 0.024 99.7 -86: (ns/day) (hour/ns) -86: Performance: 60.502 0.397 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 195.308 0.123 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1786 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.6 -86: (ns/day) (hour/ns) -86: Performance: 100.512 0.239 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.022 0.022 99.8 -86: (ns/day) (hour/ns) -86: Performance: 65.789 0.365 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.685 0.685 100.0 -86: (ns/day) (hour/ns) -86: Performance: 2.143 11.199 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.495 0.495 100.0 -86: (ns/day) (hour/ns) -86: Performance: 2.965 8.095 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.456 0.456 100.0 -86: (ns/day) (hour/ns) -86: Performance: 3.223 7.447 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.144 0.144 100.0 -86: (ns/day) (hour/ns) -86: Performance: 10.177 2.358 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4653 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.012 0.012 99.6 -86: (ns/day) (hour/ns) -86: Performance: 123.866 0.194 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 262.119 0.092 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 250.105 0.096 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 197.937 0.121 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.1 -86: (ns/day) (hour/ns) -86: Performance: 211.015 0.114 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 188.958 0.127 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1713 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.043 0.043 99.9 -86: (ns/day) (hour/ns) -86: Performance: 34.482 0.696 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.0 -86: (ns/day) (hour/ns) -86: Performance: 258.544 0.093 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.4 -86: (ns/day) (hour/ns) -86: Performance: 271.034 0.089 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.055 0.055 99.9 -86: (ns/day) (hour/ns) -86: Performance: 26.471 0.907 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 158.276 0.152 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.225 0.225 100.0 -86: (ns/day) (hour/ns) -86: Performance: 6.534 3.673 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2170 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.207 0.207 100.0 -86: (ns/day) (hour/ns) -86: Performance: 7.090 3.385 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.7 -86: (ns/day) (hour/ns) -86: Performance: 137.394 0.175 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.019 0.019 99.8 -86: (ns/day) (hour/ns) -86: Performance: 77.292 0.311 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.7 -86: (ns/day) (hour/ns) -86: Performance: 100.050 0.240 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.6 -86: (ns/day) (hour/ns) -86: Performance: 164.541 0.146 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.012 0.012 99.6 -86: (ns/day) (hour/ns) -86: Performance: 123.474 0.194 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1992 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.013 0.013 99.7 -86: (ns/day) (hour/ns) -86: Performance: 114.663 0.209 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.7 -86: (ns/day) (hour/ns) -86: Performance: 180.451 0.133 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 207.274 0.116 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.012 0.012 99.7 -86: (ns/day) (hour/ns) -86: Performance: 122.645 0.196 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.016 0.016 99.9 -86: (ns/day) (hour/ns) -86: Performance: 89.916 0.267 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: NVE simulation: will use the initial temperature of 398.997 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.8 -86: (ns/day) (hour/ns) -86: Performance: 145.972 0.164 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1720 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.014 0.014 99.7 -86: (ns/day) (hour/ns) -86: Performance: 105.425 0.228 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 204.027 0.118 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 193.164 0.124 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 139.940 0.172 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.039 0.039 99.9 -86: (ns/day) (hour/ns) -86: Performance: 38.078 0.630 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 1.025 1.025 100.0 -86: (ns/day) (hour/ns) -86: Performance: 1.432 16.755 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3161 ms) -86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 1.285 1.285 100.0 -86: (ns/day) (hour/ns) -86: Performance: 1.143 21.003 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 200.416 0.120 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 231.141 0.104 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.6 -86: (ns/day) (hour/ns) -86: Performance: 151.478 0.158 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.7 -86: (ns/day) (hour/ns) -86: Performance: 133.993 0.179 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generating 1-4 interactions: fudge = 0.5 -86: Number of degrees of freedom in T-Coupling group System is 27.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: You are using a plain Coulomb cut-off, which might produce artifacts. -86: You might want to consider using PME electrostatics. -86: -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -86: -86: Using 1 MPI thread -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'spc2' -86: 16 steps, 0.0 ps. -86: Generated 330891 of the 330891 non-bonded parameter combinations -86: -86: Generated 330891 of the 330891 1-4 parameter combinations -86: -86: Excluding 2 bonded neighbours molecule type 'SOL' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 168.645 0.142 -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2983 ms) -86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (32258 ms total) -86: -86: [----------] Global test environment tear-down -86: [==========] 13 tests from 1 test suite ran. (32282 ms total) -86: [ PASSED ] 13 tests. -86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 32.30 sec -test 87 - Start 87: MdrunCoordinationConstraintsTests2Ranks - -87: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" -87: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -87: Test timeout computed to be: 1920 -87: [==========] Running 13 tests from 1 test suite. -87: [----------] Global test environment set-up. -87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 197.8 -87: (ns/day) (hour/ns) -87: Performance: 197.265 0.122 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.6%. -87: The balanceable part of the MD step is 44%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.2 -87: (ns/day) (hour/ns) -87: Performance: 187.529 0.128 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.8%. -87: The balanceable part of the MD step is 37%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.8%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 197.6 -87: (ns/day) (hour/ns) -87: Performance: 259.514 0.092 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.1%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.4%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 196.761 0.122 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 5.1%. -87: The balanceable part of the MD step is 34%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.7%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 198.8 -87: (ns/day) (hour/ns) -87: Performance: 172.488 0.139 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.2%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.4%. -87: -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.047 0.024 199.4 -87: (ns/day) (hour/ns) -87: Performance: 62.368 0.385 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1821 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 50%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.009 198.7 -87: (ns/day) (hour/ns) -87: Performance: 156.559 0.153 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.2%. -87: The balanceable part of the MD step is 20%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 37 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 215.567 0.111 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.8%. -87: The balanceable part of the MD step is 39%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 198.2 -87: (ns/day) (hour/ns) -87: Performance: 148.073 0.162 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.1%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.7 -87: (ns/day) (hour/ns) -87: Performance: 160.977 0.149 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.6%. -87: The balanceable part of the MD step is 37%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.041 0.021 199.1 -87: (ns/day) (hour/ns) -87: Performance: 71.587 0.335 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.7%. -87: The balanceable part of the MD step is 37%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.029 0.014 198.8 -87: (ns/day) (hour/ns) -87: Performance: 102.010 0.235 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1782 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.0%. -87: The balanceable part of the MD step is 50%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.5 -87: (ns/day) (hour/ns) -87: Performance: 162.744 0.147 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.5%. -87: The balanceable part of the MD step is 45%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.2%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.3 -87: (ns/day) (hour/ns) -87: Performance: 194.334 0.123 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 37%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 197.3 -87: (ns/day) (hour/ns) -87: Performance: 221.226 0.108 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 198.607 0.121 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.5%. -87: The balanceable part of the MD step is 38%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.3%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.026 0.013 198.7 -87: (ns/day) (hour/ns) -87: Performance: 111.980 0.214 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 197.7 -87: (ns/day) (hour/ns) -87: Performance: 199.172 0.120 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1811 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.3 -87: (ns/day) (hour/ns) -87: Performance: 164.872 0.146 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 198.6 -87: (ns/day) (hour/ns) -87: Performance: 167.594 0.143 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.008 198.5 -87: (ns/day) (hour/ns) -87: Performance: 176.279 0.136 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 197.7 -87: (ns/day) (hour/ns) -87: Performance: 215.443 0.111 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 197.8 -87: (ns/day) (hour/ns) -87: Performance: 180.203 0.133 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.162 0.581 200.0 -87: (ns/day) (hour/ns) -87: Performance: 2.528 9.495 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2634 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.899 0.450 200.0 -87: (ns/day) (hour/ns) -87: Performance: 3.265 7.350 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.983 0.492 200.0 -87: (ns/day) (hour/ns) -87: Performance: 2.987 8.035 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 3.226 1.613 200.0 -87: (ns/day) (hour/ns) -87: Performance: 0.911 26.354 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 2.449 1.225 200.0 -87: (ns/day) (hour/ns) -87: Performance: 1.199 20.012 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 2.631 1.316 200.0 -87: (ns/day) (hour/ns) -87: Performance: 1.116 21.499 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.970 0.985 200.0 -87: (ns/day) (hour/ns) -87: Performance: 1.491 16.096 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (9661 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 2.172 1.086 200.0 -87: (ns/day) (hour/ns) -87: Performance: 1.353 17.742 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.005 0.503 200.0 -87: (ns/day) (hour/ns) -87: Performance: 2.922 8.214 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.614 0.307 199.9 -87: (ns/day) (hour/ns) -87: Performance: 4.785 5.016 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.3 -87: (ns/day) (hour/ns) -87: Performance: 205.329 0.117 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 198.0 -87: (ns/day) (hour/ns) -87: Performance: 142.065 0.169 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.3 -87: (ns/day) (hour/ns) -87: Performance: 183.860 0.131 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4030 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 2.193 1.096 200.0 -87: (ns/day) (hour/ns) -87: Performance: 1.340 17.917 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.393 0.697 200.0 -87: (ns/day) (hour/ns) -87: Performance: 2.108 11.385 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.6 -87: (ns/day) (hour/ns) -87: Performance: 240.997 0.100 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.1 -87: (ns/day) (hour/ns) -87: Performance: 198.614 0.121 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 197.8 -87: (ns/day) (hour/ns) -87: Performance: 176.314 0.136 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 198.3 -87: (ns/day) (hour/ns) -87: Performance: 169.408 0.142 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3897 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.024 0.012 198.6 -87: (ns/day) (hour/ns) -87: Performance: 123.020 0.195 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 204.321 0.117 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.4 -87: (ns/day) (hour/ns) -87: Performance: 301.982 0.079 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.010 198.3 -87: (ns/day) (hour/ns) -87: Performance: 152.944 0.157 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.075 0.038 199.3 -87: (ns/day) (hour/ns) -87: Performance: 38.889 0.617 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.7 -87: (ns/day) (hour/ns) -87: Performance: 180.142 0.133 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1772 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.5 -87: (ns/day) (hour/ns) -87: Performance: 205.439 0.117 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 197.7 -87: (ns/day) (hour/ns) -87: Performance: 222.428 0.108 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.217 0.109 199.9 -87: (ns/day) (hour/ns) -87: Performance: 13.512 1.776 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.571 0.286 199.9 -87: (ns/day) (hour/ns) -87: Performance: 5.143 4.667 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.320 0.160 199.9 -87: (ns/day) (hour/ns) -87: Performance: 9.180 2.614 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.083 0.042 199.7 -87: (ns/day) (hour/ns) -87: Performance: 35.176 0.682 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2327 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.1%. -87: The balanceable part of the MD step is 57%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.2%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.535 0.267 199.9 -87: (ns/day) (hour/ns) -87: Performance: 5.492 4.370 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.9%. -87: The balanceable part of the MD step is 56%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 196.8 -87: (ns/day) (hour/ns) -87: Performance: 187.591 0.128 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.7%. -87: The balanceable part of the MD step is 50%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.9%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 196.7 -87: (ns/day) (hour/ns) -87: Performance: 178.550 0.134 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.8%. -87: The balanceable part of the MD step is 44%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.041 0.020 198.5 -87: (ns/day) (hour/ns) -87: Performance: 71.938 0.334 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.4%. -87: The balanceable part of the MD step is 45%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 198.3 -87: (ns/day) (hour/ns) -87: Performance: 138.577 0.173 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 4.2%. -87: The balanceable part of the MD step is 46%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.9%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.028 0.014 198.7 -87: (ns/day) (hour/ns) -87: Performance: 103.200 0.233 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2075 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.5%. -87: The balanceable part of the MD step is 57%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.3%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.022 0.011 197.9 -87: (ns/day) (hour/ns) -87: Performance: 134.782 0.178 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.5%. -87: The balanceable part of the MD step is 56%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.010 197.3 -87: (ns/day) (hour/ns) -87: Performance: 153.449 0.156 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB got disabled because it was unsuitable to use. -87: Average load imbalance: 4.3%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.2%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.022 0.011 197.3 -87: (ns/day) (hour/ns) -87: Performance: 130.761 0.184 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 49%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.025 0.013 198.0 -87: (ns/day) (hour/ns) -87: Performance: 117.265 0.205 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.2%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.0 -87: (ns/day) (hour/ns) -87: Performance: 161.534 0.149 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: NVE simulation: will use the initial temperature of 398.997 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.9%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.200 0.100 199.7 -87: (ns/day) (hour/ns) -87: Performance: 14.646 1.639 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1897 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.028 0.014 198.3 -87: (ns/day) (hour/ns) -87: Performance: 102.346 0.234 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.2 -87: (ns/day) (hour/ns) -87: Performance: 160.497 0.150 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.023 0.012 197.7 -87: (ns/day) (hour/ns) -87: Performance: 127.051 0.189 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.032 0.016 198.4 -87: (ns/day) (hour/ns) -87: Performance: 92.200 0.260 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.028 0.014 198.2 -87: (ns/day) (hour/ns) -87: Performance: 103.618 0.232 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.025 0.013 197.3 -87: (ns/day) (hour/ns) -87: Performance: 115.869 0.207 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1855 ms) -87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.028 0.014 198.2 -87: (ns/day) (hour/ns) -87: Performance: 104.134 0.230 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.467 0.234 199.9 -87: (ns/day) (hour/ns) -87: Performance: 6.283 3.820 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.082 0.541 199.9 -87: (ns/day) (hour/ns) -87: Performance: 2.715 8.840 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.231 0.616 199.8 -87: (ns/day) (hour/ns) -87: Performance: 2.383 10.070 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 3.836 1.918 200.0 -87: (ns/day) (hour/ns) -87: Performance: 0.766 31.347 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generating 1-4 interactions: fudge = 0.5 -87: Number of degrees of freedom in T-Coupling group System is 27.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: You are using a plain Coulomb cut-off, which might produce artifacts. -87: You might want to consider using PME electrostatics. -87: -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -87: -87: Using 2 MPI threads -87: Using 1 OpenMP thread per tMPI thread -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'spc2' -87: 16 steps, 0.0 ps. -87: Generated 330891 of the 330891 non-bonded parameter combinations -87: -87: Generated 330891 of the 330891 1-4 parameter combinations -87: -87: Excluding 2 bonded neighbours molecule type 'SOL' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 3.611 1.806 200.0 -87: (ns/day) (hour/ns) -87: Performance: 0.813 29.503 -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file -87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (7940 ms) -87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (43510 ms total) -87: -87: [----------] Global test environment tear-down -87: [==========] 13 tests from 1 test suite ran. (43538 ms total) -87: [ PASSED ] 13 tests. -87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 43.55 sec -test 88 - Start 88: MdrunFEPTests - -88: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" -88: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -88: Test timeout computed to be: 600 -88: [==========] Running 14 tests from 2 test suites. -88: [----------] Global test environment set-up. -88: [----------] 2 tests from ExpandedEnsembleTest -88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 79.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 2 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 16 steps, 0.0 ps. -88: Generated 2485 of the 2485 non-bonded parameter combinations -88: -88: Generated 2485 of the 2485 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'nonanol' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 2.958 1.479 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.993 24.166 -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps -88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -88: -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 5.602 2.801 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.278 86.450 -88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (4313 ms) -88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 79.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 2 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun '30 atom system in water' -88: 1 steps, 0.0 ps. -88: Generated 2485 of the 2485 non-bonded parameter combinations -88: -88: Generated 2485 of the 2485 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'nonanol' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 1.323 0.661 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.261 91.862 -88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (692 ms) -88: [----------] 2 tests from ExpandedEnsembleTest (5006 ms total) -88: -88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to 1605352447 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 4.665 2.332 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.778 30.852 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) -88: -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (2547 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -191439428 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 3.990 1.995 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.909 26.394 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (2170 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 4 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -1880637618 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 1.725 0.862 200.0 -88: (ns/day) (hour/ns) -88: Performance: 2.104 11.408 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (996 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: NOTE 3 [file topol.top, line 155]: -88: System has non-zero total charge: 1.000000 -88: Total charge should normally be an integer. See -88: https://manual.gromacs.org/current/user-guide/floating-point.html -88: for discussion on how close it should be to an integer. -88: -88: -88: -88: -88: WARNING 2 [file topol.top, line 155]: -88: You are using Ewald electrostatics in a system with net charge. This can -88: lead to severe artifacts, such as ions moving into regions with low -88: dielectric, due to the uniform background charge. We suggest to -88: neutralize your system with counter ions, possibly in combination with a -88: physiological salt concentration. -88: -88: Setting the LD random seed to -20971733 -88: -88: Generated 171 of the 171 non-bonded parameter combinations -88: -88: Generated 171 of the 171 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'NA' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -88: Charge -88: J. Chem. Theory Comput. (2014) -88: DOI: 10.1021/ct400626b -88: -------- -------- --- Thank You --- -------- -------- -88: -88: Number of degrees of freedom in T-Coupling group System is 358.00 -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 5 NOTEs -88: -88: There were 2 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: There are: 1 Ion residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.95 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 3.109 1.555 200.0 -88: (ns/day) (hour/ns) -88: Performance: 1.167 20.563 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (1920 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: NOTE 3 [file topol.top, line 165]: -88: System has non-zero total charge: 1.000000 -88: Total charge should normally be an integer. See -88: https://manual.gromacs.org/current/user-guide/floating-point.html -88: for discussion on how close it should be to an integer. -88: -88: -88: -88: -88: WARNING 2 [file topol.top, line 165]: -88: You are using Ewald electrostatics in a system with net charge. This can -88: lead to severe artifacts, such as ions moving into regions with low -88: dielectric, due to the uniform background charge. We suggest to -88: neutralize your system with counter ions, possibly in combination with a -88: physiological salt concentration. -88: -88: Setting the LD random seed to -539887974 -88: -88: Generated 190 of the 190 non-bonded parameter combinations -88: -88: Generated 190 of the 190 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'NA' -88: -88: turning H bonds into constraints... -88: -88: Excluding 1 bonded neighbours molecule type 'CL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'CL' -88: -88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -88: Charge -88: J. Chem. Theory Comput. (2014) -88: DOI: 10.1021/ct400626b -88: -------- -------- --- Thank You --- -------- -------- -88: -88: Number of degrees of freedom in T-Coupling group System is 361.00 -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 5 NOTEs -88: -88: There were 2 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: There are: 2 Ion residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.95 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 5.343 2.672 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.679 35.339 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (2908 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: -88: For proper sampling of the (nearly) decoupled state, stochastic dynamics -88: should be used -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off -88: and vdw_modifier=Force-switch -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 4 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 100 steps, 0.1 ps. -88: Setting the LD random seed to -885088771 -88: -88: Generated 153 of the 153 non-bonded parameter combinations -88: -88: Generated 153 of the 153 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Coupling 1 copies of molecule type 'ASN' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 5.373 2.687 200.0 -88: (ns/day) (hour/ns) -88: Performance: 3.248 7.389 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (3004 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: WARNING 2 [file topol.top, line 72]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 8 1'. -88: -88: -88: WARNING 3 [file topol.top, line 73]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 9 1'. -88: -88: -88: WARNING 4 [file topol.top, line 98]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '6 5 7 1'. -88: -88: -88: WARNING 5 [file topol.top, line 99]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 8 1'. -88: -88: -88: WARNING 6 [file topol.top, line 100]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 9 1'. -88: -88: -88: WARNING 7 [file topol.top, line 101]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '8 7 9 1'. -88: -88: -88: WARNING 8 [file topol.top, line 111]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 8 3'. -88: -88: -88: WARNING 9 [file topol.top, line 112]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 9 3'. -88: -88: -88: WARNING 10 [file topol.top, line 113]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 8 3'. -88: -88: -88: WARNING 11 [file topol.top, line 114]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 9 3'. -88: -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 2 NOTEs -88: -88: There were 11 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -109051921 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 3.416 1.708 200.0 -88: (ns/day) (hour/ns) -88: Performance: 1.062 22.595 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (2007 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: WARNING 2 [file topol.top, line 72]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 8 1'. -88: -88: -88: WARNING 3 [file topol.top, line 73]: -88: No default Bond types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '7 9 1'. -88: -88: -88: WARNING 4 [file topol.top, line 98]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '6 5 7 1'. -88: -88: -88: WARNING 5 [file topol.top, line 99]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 8 1'. -88: -88: -88: WARNING 6 [file topol.top, line 100]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '5 7 9 1'. -88: -88: -88: WARNING 7 [file topol.top, line 101]: -88: No default Angle types for perturbed atoms in interaction, using normal -88: values. The interaction was -88: '8 7 9 1'. -88: -88: -88: WARNING 8 [file topol.top, line 111]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 8 3'. -88: -88: -88: WARNING 9 [file topol.top, line 112]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '1 5 7 9 3'. -88: -88: -88: WARNING 10 [file topol.top, line 113]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 8 3'. -88: -88: -88: WARNING 11 [file topol.top, line 114]: -88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -88: normal values. The interaction was -88: '6 5 7 9 3'. -88: -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: Removing center of mass motion in the presence of position restraints -88: might cause artifacts. When you are using position restraints to -88: equilibrate a macro-molecule, the artifacts are usually negligible. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There were 11 WARNINGs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -80218377 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.511 0.256 199.9 -88: (ns/day) (hour/ns) -88: Performance: 7.093 3.384 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (533 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 2 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to 2146399929 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.86 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 4.628 2.314 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.784 30.611 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (2613 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: There was 1 NOTE -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.428 0.214 199.9 -88: (ns/day) (hour/ns) -88: Performance: 8.479 2.830 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: Setting the LD random seed to -1680635917 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.86 -88: -88: This run will generate roughly 0 Mb of data -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (460 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -60688677 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.92 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 3.725 1.862 200.0 -88: (ns/day) (hour/ns) -88: Performance: 0.974 24.635 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (2084 ms) -88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: With PME there is a minor soft core effect present at the cut-off, -88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -88: energy conservation, but usually other effects dominate. With a common -88: sigma value of 0.34 nm the fraction of the particle-particle potential at -88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -88: -88: -88: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: The Berendsen thermostat does not generate the correct kinetic energy -88: distribution, and should not be used for new production simulations (in -88: our opinion). We would recommend the V-rescale thermostat. -88: -88: Generating 1-4 interactions: fudge = 0.5 -88: Number of degrees of freedom in T-Coupling group System is 355.00 -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: The optimal PME mesh load for parallel simulations is below 0.5 -88: and for highly parallel simulations between 0.25 and 0.33, -88: for higher performance, increase the cut-off and the PME grid spacing. -88: -88: -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -88: For free energy simulations, the optimal load limit increases from 0.5 to -88: 0.667 -88: -88: -88: -88: There were 3 NOTEs -88: -88: There was 1 WARNING -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -88: Changing nstlist from 10 to 100, rlist from 1 to 1 -88: -88: Using 1 MPI thread -88: Using 2 OpenMP threads -88: -88: -88: NOTE: The number of threads is not equal to the number of (logical) cpus -88: and the -pin option is set to auto: will not pin threads to cpus. -88: This can lead to significant performance degradation. -88: Consider using -pin on (and -pinoffset in case you run multiple jobs). -88: starting mdrun 'AA' -88: 20 steps, 0.0 ps. -88: Setting the LD random seed to -537140489 -88: -88: Generated 136 of the 136 non-bonded parameter combinations -88: -88: Generated 136 of the 136 1-4 parameter combinations -88: -88: Excluding 3 bonded neighbours molecule type 'ASN' -88: -88: turning H bonds into constraints... -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: turning H bonds into constraints... -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' -88: Analysing residue names: -88: There are: 1 Protein residues -88: There are: 56 Water residues -88: Analysing Protein... -88: -88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 -88: -88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: Calculating fourier grid dimensions for X Y Z -88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -88: -88: Estimate for the relative computational load of the PME mesh part: 0.86 -88: -88: This run will generate roughly 0 Mb of data -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 1.427 0.713 200.0 -88: (ns/day) (hour/ns) -88: Performance: 2.543 9.436 -88: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 -88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (869 ms) -88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (22123 ms total) -88: -88: [----------] Global test environment tear-down -88: [==========] 14 tests from 2 test suites ran. (27204 ms total) -88: [ PASSED ] 14 tests. -88/92 Test #88: MdrunFEPTests ............................. Passed 27.22 sec -test 89 - Start 89: MdrunPullTests - -89: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" -89: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -89: Test timeout computed to be: 600 -89: [==========] Running 4 tests from 1 test suite. -89: [----------] Global test environment set-up. -89: [----------] 4 tests from PullTest/PullIntegrationTest -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.600 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 2.383 1.191 200.0 -89: (ns/day) (hour/ns) -89: Performance: 1.523 15.760 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (1600 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.301 nm 0.400 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 3.862 1.931 200.0 -89: (ns/day) (hour/ns) -89: Performance: 0.940 25.542 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (2450 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Pull group 3 'r_3' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1292.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.357 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.500 nm -89: 1 3 2 -89: 3 3 8 0.331 nm 0.400 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.943 0.472 200.0 -89: (ns/day) (hour/ns) -89: Performance: 3.847 6.238 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (890 ms) -89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 -89: Generating 1-4 interactions: fudge = 0.5 -89: Pull group 1 'r_1' has 3 atoms -89: Pull group 2 'r_2' has 3 atoms -89: Number of degrees of freedom in T-Coupling group System is 1293.00 -89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: -89: NVE simulation: will use the initial temperature of 303.122 K for -89: determining the Verlet buffer size -89: -89: Pull group natoms pbc atom distance at start reference at t=0 -89: 1 3 2 -89: 2 3 5 0.575 nm 0.000 nm -89: 1 3 2 -89: 2 3 5 0.050 nm 0.000 nm -89: -89: There was 1 NOTE -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 1 MPI thread -89: Using 2 OpenMP threads -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 20 steps, 0.0 ps. -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 1.690 0.845 200.0 -89: (ns/day) (hour/ns) -89: Performance: 2.148 11.175 -89: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (1217 ms) -89: [----------] 4 tests from PullTest/PullIntegrationTest (6159 ms total) -89: -89: [----------] Global test environment tear-down -89: [==========] 4 tests from 1 test suite ran. (6179 ms total) -89: [ PASSED ] 4 tests. -89/92 Test #89: MdrunPullTests ............................ Passed 6.19 sec -test 90 - Start 90: MdrunRotationTests - -90: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" -90: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -90: Test timeout computed to be: 600 -90: [==========] Running 12 tests from 1 test suite. -90: [----------] Global test environment set-up. -90: [----------] 12 tests from RotationWorks/RotationTest -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 -90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: trr version: GMX_trn_file (single precision) -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1011384341 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 9.020 4.510 200.0 -90: (ns/day) (hour/ns) -90: Performance: 0.996 24.091 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (4815 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 -90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to 2080373961 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 2.251 1.125 200.0 -90: (ns/day) (hour/ns) -90: Performance: 3.992 6.011 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (1133 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 -90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1386218273 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 6.063 3.031 200.0 -90: (ns/day) (hour/ns) -90: Performance: 1.482 16.193 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (3162 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 -90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -432406529 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 3.496 1.748 200.0 -90: (ns/day) (hour/ns) -90: Performance: 2.570 9.339 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (1874 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 -90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -8462598 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 4.678 2.339 200.0 -90: (ns/day) (hour/ns) -90: Performance: 1.921 12.496 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (2360 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 -90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -572561699 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 1.801 0.901 200.0 -90: (ns/day) (hour/ns) -90: Performance: 4.988 4.812 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (908 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 -90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to 1811405163 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 1.611 0.806 200.0 -90: (ns/day) (hour/ns) -90: Performance: 5.576 4.304 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (817 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 -90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1905268365 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 1.784 0.892 200.0 -90: (ns/day) (hour/ns) -90: Performance: 5.035 4.766 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (916 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 -90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1958766521 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 1.661 0.831 200.0 -90: (ns/day) (hour/ns) -90: Performance: 5.408 4.438 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (863 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 -90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1888854529 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 5.588 2.794 200.0 -90: (ns/day) (hour/ns) -90: Performance: 1.608 14.924 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (2818 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 -90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -1075839015 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 3.524 1.762 200.0 -90: (ns/day) (hour/ns) -90: Performance: 2.550 9.413 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (2011 ms) -90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 -90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Rotation group 0 'system' has 4 atoms -90: Number of degrees of freedom in T-Coupling group rest is 9.00 -90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -90: NVE simulation with an initial temperature of zero: will use a Verlet -90: buffer of 10%. Check your energy drift! -90: -90: Enforced rotation: group 0 has 4 reference positions. -90: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -90: Can not increase nstlist because an NVE ensemble is used -90: Using 1 MPI thread -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -90: 25 steps, 0.1 ps. -90: Setting the LD random seed to -658433 -90: -90: Generated 1 of the 1 non-bonded parameter combinations -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonA' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonB' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonC' -90: -90: Excluding 1 bonded neighbours molecule type 'ArgonD' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 8.435 4.218 200.0 -90: (ns/day) (hour/ns) -90: Performance: 1.065 22.530 -90: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file -90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (4399 ms) -90: [----------] 12 tests from RotationWorks/RotationTest (26084 ms total) -90: -90: [----------] Global test environment tear-down -90: [==========] 12 tests from 1 test suite ran. (26106 ms total) -90: [ PASSED ] 12 tests. -90/92 Test #90: MdrunRotationTests ........................ Passed 26.37 sec -test 91 - Start 91: MdrunSimulatorComparison - -91: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" -91: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -91: Test timeout computed to be: 600 -91: [==========] Running 94 tests from 4 test suites. -91: [----------] Global test environment set-up. -91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: NVE simulation: will use the initial temperature of 68.810 K for -91: determining the Verlet buffer size -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.383 0.691 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.124 11.299 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 2.443 1.222 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.202 19.964 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) -91: -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (2211 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: NVE simulation: will use the initial temperature of 68.810 K for -91: determining the Verlet buffer size -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 3.391 1.696 200.0 -91: (ns/day) (hour/ns) -91: Performance: 0.866 27.709 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.304 0.652 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.252 10.655 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (2458 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 3.557 1.779 200.0 -91: (ns/day) (hour/ns) -91: Performance: 0.826 29.061 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.911 0.956 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.537 15.617 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (2891 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.038 0.019 199.6 -91: (ns/day) (hour/ns) -91: Performance: 78.027 0.308 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.056 0.028 199.6 -91: (ns/day) (hour/ns) -91: Performance: 52.155 0.460 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (56 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.023 0.012 199.2 -91: (ns/day) (hour/ns) -91: Performance: 124.883 0.192 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.023 0.012 199.1 -91: (ns/day) (hour/ns) -91: Performance: 127.033 0.189 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (34 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.026 0.013 199.2 -91: (ns/day) (hour/ns) -91: Performance: 111.940 0.214 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.019 0.009 198.9 -91: (ns/day) (hour/ns) -91: Performance: 155.394 0.154 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (32 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: -91: WARNING 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There were 2 WARNINGs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.065 0.032 199.7 -91: (ns/day) (hour/ns) -91: Performance: 45.372 0.529 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.234 0.117 199.9 -91: (ns/day) (hour/ns) -91: Performance: 12.534 1.915 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (161 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.049 0.025 199.6 -91: (ns/day) (hour/ns) -91: Performance: 59.892 0.401 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.019 0.009 199.0 -91: (ns/day) (hour/ns) -91: Performance: 156.452 0.153 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (54 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: MTTK coupling is deprecated and will soon be removed -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.053 0.027 199.6 -91: (ns/day) (hour/ns) -91: Performance: 54.945 0.437 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.049 0.025 199.5 -91: (ns/day) (hour/ns) -91: Performance: 59.270 0.405 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (358 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.024 0.012 199.2 -91: (ns/day) (hour/ns) -91: Performance: 122.902 0.195 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.027 0.013 198.9 -91: (ns/day) (hour/ns) -91: Performance: 109.969 0.218 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (36 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.031 0.016 199.3 -91: (ns/day) (hour/ns) -91: Performance: 93.763 0.256 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.021 0.011 198.6 -91: (ns/day) (hour/ns) -91: Performance: 136.164 0.176 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (36 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: -91: MTTK coupling is deprecated and will soon be removed -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.024 0.012 198.9 -91: (ns/day) (hour/ns) -91: Performance: 123.160 0.195 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.021 0.011 198.8 -91: (ns/day) (hour/ns) -91: Performance: 137.167 0.175 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (36 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.098 0.049 199.7 -91: (ns/day) (hour/ns) -91: Performance: 30.023 0.799 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.179 0.090 199.8 -91: (ns/day) (hour/ns) -91: Performance: 16.387 1.465 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (161 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.117 0.059 199.8 -91: (ns/day) (hour/ns) -91: Performance: 25.090 0.957 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.244 0.122 199.9 -91: (ns/day) (hour/ns) -91: Performance: 12.037 1.994 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (194 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.051 0.026 199.6 -91: (ns/day) (hour/ns) -91: Performance: 56.996 0.421 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.022 0.011 199.0 -91: (ns/day) (hour/ns) -91: Performance: 133.309 0.180 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (54 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: Center of mass removal not necessary for Andersen. All velocities of -91: coupled groups are rerandomized periodically, so flying ice cube errors -91: will not occur. -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.290 0.145 199.9 -91: (ns/day) (hour/ns) -91: Performance: 10.137 2.368 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.067 0.034 199.7 -91: (ns/day) (hour/ns) -91: Performance: 43.747 0.549 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (213 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: Center of mass removal not necessary for Andersen. All velocities of -91: coupled groups are rerandomized periodically, so flying ice cube errors -91: will not occur. -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.184 0.092 199.9 -91: (ns/day) (hour/ns) -91: Performance: 15.926 1.507 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.031 0.016 199.1 -91: (ns/day) (hour/ns) -91: Performance: 93.819 0.256 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (132 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: Center of mass removal not necessary for Andersen. All velocities of -91: coupled groups are rerandomized periodically, so flying ice cube errors -91: will not occur. -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.082 0.041 199.7 -91: (ns/day) (hour/ns) -91: Performance: 35.825 0.670 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.047 0.024 199.5 -91: (ns/day) (hour/ns) -91: Performance: 62.223 0.386 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (78 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: NVE simulation: will use the initial temperature of 398.997 K for -91: determining the Verlet buffer size -91: -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.778 0.389 200.0 -91: (ns/day) (hour/ns) -91: Performance: 3.773 6.361 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.030 0.015 199.3 -91: (ns/day) (hour/ns) -91: Performance: 96.663 0.248 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (699 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: -91: NVE simulation: will use the initial temperature of 398.997 K for -91: determining the Verlet buffer size -91: -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.112 0.056 199.9 -91: (ns/day) (hour/ns) -91: Performance: 26.203 0.916 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.080 0.040 199.6 -91: (ns/day) (hour/ns) -91: Performance: 36.639 0.655 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (382 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.102 0.051 199.8 -91: (ns/day) (hour/ns) -91: Performance: 28.758 0.835 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.269 0.134 199.9 -91: (ns/day) (hour/ns) -91: Performance: 10.932 2.195 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (481 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.500 0.250 200.0 -91: (ns/day) (hour/ns) -91: Performance: 5.870 4.089 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.022 0.011 198.9 -91: (ns/day) (hour/ns) -91: Performance: 135.454 0.177 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (554 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 3.138 1.569 200.0 -91: (ns/day) (hour/ns) -91: Performance: 0.936 25.634 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 2.411 1.206 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.218 19.700 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (3148 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.145 0.572 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.566 9.353 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.613 0.306 200.0 -91: (ns/day) (hour/ns) -91: Performance: 4.794 5.006 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (1268 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: -91: WARNING 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There were 2 WARNINGs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 2.619 1.309 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.122 21.395 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.603 0.301 200.0 -91: (ns/day) (hour/ns) -91: Performance: 4.873 4.926 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (1953 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.039 0.019 199.6 -91: (ns/day) (hour/ns) -91: Performance: 76.123 0.315 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.028 0.014 199.3 -91: (ns/day) (hour/ns) -91: Performance: 104.530 0.230 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (334 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.105 0.053 199.8 -91: (ns/day) (hour/ns) -91: Performance: 27.969 0.858 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.078 0.039 199.7 -91: (ns/day) (hour/ns) -91: Performance: 37.751 0.636 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (377 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.731 0.366 200.0 -91: (ns/day) (hour/ns) -91: Performance: 4.018 5.973 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.057 0.029 199.6 -91: (ns/day) (hour/ns) -91: Performance: 51.174 0.469 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (678 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.144 0.072 199.9 -91: (ns/day) (hour/ns) -91: Performance: 20.439 1.174 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.118 0.059 199.8 -91: (ns/day) (hour/ns) -91: Performance: 24.911 0.963 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (439 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.489 0.245 200.0 -91: (ns/day) (hour/ns) -91: Performance: 6.003 3.998 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.073 0.037 199.7 -91: (ns/day) (hour/ns) -91: Performance: 39.949 0.601 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (572 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: -91: Andersen temperature control methods assume nsttcouple = 1; there is no -91: need for larger nsttcouple > 1, since no global parameters are computed. -91: nsttcouple has been reset to 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.172 0.086 199.9 -91: (ns/day) (hour/ns) -91: Performance: 17.058 1.407 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.112 0.056 199.8 -91: (ns/day) (hour/ns) -91: Performance: 26.259 0.914 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (460 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 -91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) -91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (20557 ms total) -91: -91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: NVE simulation: will use the initial temperature of 68.810 K for -91: determining the Verlet buffer size -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.045 0.023 199.5 -91: (ns/day) (hour/ns) -91: Performance: 65.092 0.369 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.071 0.035 199.8 -91: (ns/day) (hour/ns) -91: Performance: 41.524 0.578 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (71 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: -91: NVE simulation: will use the initial temperature of 68.810 K for -91: determining the Verlet buffer size -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.054 0.027 199.4 -91: (ns/day) (hour/ns) -91: Performance: 53.839 0.446 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.055 0.027 199.7 -91: (ns/day) (hour/ns) -91: Performance: 53.651 0.447 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (67 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: -91: NVE simulation: will use the initial temperature of 68.810 K for -91: determining the Verlet buffer size -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.168 0.084 199.9 -91: (ns/day) (hour/ns) -91: Performance: 17.467 1.374 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 2.473 1.237 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.188 20.205 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (1502 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.180 0.090 199.9 -91: (ns/day) (hour/ns) -91: Performance: 16.342 1.469 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.078 0.039 199.8 -91: (ns/day) (hour/ns) -91: Performance: 37.828 0.634 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (150 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.056 0.028 199.6 -91: (ns/day) (hour/ns) -91: Performance: 52.298 0.459 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.183 0.091 199.9 -91: (ns/day) (hour/ns) -91: Performance: 16.075 1.493 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (138 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.114 0.057 199.8 -91: (ns/day) (hour/ns) -91: Performance: 25.790 0.931 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.151 0.075 199.9 -91: (ns/day) (hour/ns) -91: Performance: 19.471 1.233 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (155 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.124 0.062 199.8 -91: (ns/day) (hour/ns) -91: Performance: 23.638 1.015 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.077 0.039 199.7 -91: (ns/day) (hour/ns) -91: Performance: 38.086 0.630 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (116 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.308 0.154 199.9 -91: (ns/day) (hour/ns) -91: Performance: 9.542 2.515 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.229 0.115 199.9 -91: (ns/day) (hour/ns) -91: Performance: 12.808 1.874 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (284 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.059 0.030 199.6 -91: (ns/day) (hour/ns) -91: Performance: 49.429 0.486 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.501 0.250 199.9 -91: (ns/day) (hour/ns) -91: Performance: 5.867 4.090 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (295 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: -91: WARNING 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There were 2 WARNINGs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.338 0.169 199.9 -91: (ns/day) (hour/ns) -91: Performance: 8.684 2.764 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.187 0.094 199.9 -91: (ns/day) (hour/ns) -91: Performance: 15.659 1.533 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (289 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 2 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.025 0.013 199.2 -91: (ns/day) (hour/ns) -91: Performance: 116.515 0.206 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.128 0.064 199.8 -91: (ns/day) (hour/ns) -91: Performance: 22.860 1.050 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (95 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.061 0.030 199.6 -91: (ns/day) (hour/ns) -91: Performance: 48.245 0.497 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.073 0.037 199.7 -91: (ns/day) (hour/ns) -91: Performance: 40.143 0.598 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (103 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.082 0.041 199.7 -91: (ns/day) (hour/ns) -91: Performance: 35.881 0.669 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.054 0.027 199.6 -91: (ns/day) (hour/ns) -91: Performance: 53.961 0.445 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (83 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.087 0.043 199.7 -91: (ns/day) (hour/ns) -91: Performance: 33.814 0.710 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.327 0.163 199.9 -91: (ns/day) (hour/ns) -91: Performance: 8.991 2.669 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (252 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Number of degrees of freedom in T-Coupling group System is 33.00 -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: Generated 1 of the 1 non-bonded parameter combinations -91: -91: Excluding 1 bonded neighbours molecule type 'Argon' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.207 0.103 199.9 -91: (ns/day) (hour/ns) -91: Performance: 14.195 1.691 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'Argon' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.298 0.149 199.9 -91: (ns/day) (hour/ns) -91: Performance: 9.850 2.436 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (282 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: NVE simulation: will use the initial temperature of 398.997 K for -91: determining the Verlet buffer size -91: -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.108 0.054 199.8 -91: (ns/day) (hour/ns) -91: Performance: 27.192 0.883 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.192 0.096 199.9 -91: (ns/day) (hour/ns) -91: Performance: 15.323 1.566 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (450 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: -91: NVE simulation: will use the initial temperature of 398.997 K for -91: determining the Verlet buffer size -91: -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.113 0.057 199.8 -91: (ns/day) (hour/ns) -91: Performance: 25.982 0.924 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.150 0.075 199.8 -91: (ns/day) (hour/ns) -91: Performance: 19.626 1.223 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (465 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: NVE simulation: will use the initial temperature of 398.997 K for -91: determining the Verlet buffer size -91: -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.069 0.035 199.7 -91: (ns/day) (hour/ns) -91: Performance: 42.388 0.566 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.178 0.089 199.9 -91: (ns/day) (hour/ns) -91: Performance: 16.457 1.458 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (423 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.055 0.028 199.6 -91: (ns/day) (hour/ns) -91: Performance: 52.936 0.453 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.087 0.044 199.7 -91: (ns/day) (hour/ns) -91: Performance: 33.585 0.715 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (391 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.084 0.042 199.7 -91: (ns/day) (hour/ns) -91: Performance: 34.947 0.687 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.102 0.051 199.8 -91: (ns/day) (hour/ns) -91: Performance: 28.750 0.835 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (396 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.118 0.059 199.8 -91: (ns/day) (hour/ns) -91: Performance: 24.905 0.964 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.214 0.107 199.9 -91: (ns/day) (hour/ns) -91: Performance: 13.700 1.752 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (471 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.981 0.491 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.993 8.018 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.147 0.074 199.9 -91: (ns/day) (hour/ns) -91: Performance: 19.973 1.202 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (861 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.771 0.885 200.0 -91: (ns/day) (hour/ns) -91: Performance: 1.659 14.467 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 3.837 1.918 200.0 -91: (ns/day) (hour/ns) -91: Performance: 0.766 31.346 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (3572 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.106 0.053 199.7 -91: (ns/day) (hour/ns) -91: Performance: 27.789 0.864 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.065 0.033 199.6 -91: (ns/day) (hour/ns) -91: Performance: 44.912 0.534 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (380 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: -91: WARNING 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There were 2 WARNINGs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.041 0.521 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.821 8.507 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 1.224 0.612 200.0 -91: (ns/day) (hour/ns) -91: Performance: 2.400 10.000 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (1692 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: The Berendsen thermostat does not generate the correct kinetic energy -91: distribution, and should not be used for new production simulations (in -91: our opinion). We would recommend the V-rescale thermostat. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 3 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.311 0.156 199.9 -91: (ns/day) (hour/ns) -91: Performance: 9.426 2.546 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.438 0.219 199.9 -91: (ns/day) (hour/ns) -91: Performance: 6.712 3.576 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (682 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.064 0.032 199.5 -91: (ns/day) (hour/ns) -91: Performance: 45.550 0.527 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.231 0.116 199.9 -91: (ns/day) (hour/ns) -91: Performance: 12.693 1.891 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (449 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.256 0.128 199.9 -91: (ns/day) (hour/ns) -91: Performance: 11.474 2.092 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.088 0.044 199.7 -91: (ns/day) (hour/ns) -91: Performance: 33.417 0.718 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (800 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: -91: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: -91: The Berendsen barostat does not generate any strictly correct ensemble, -91: and should not be used for new production simulations (in our opinion). -91: We recommend using the C-rescale barostat instead. -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: -91: There was 1 WARNING -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.064 0.032 199.7 -91: (ns/day) (hour/ns) -91: Performance: 45.999 0.522 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.114 0.057 199.8 -91: (ns/day) (hour/ns) -91: Performance: 25.840 0.929 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (389 ms) -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -91: 1 -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Number of degrees of freedom in T-Coupling group System is 27.00 -91: -91: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: -91: You are using a plain Coulomb cut-off, which might produce artifacts. -91: You might want to consider using PME electrostatics. -91: -91: -91: -91: There were 4 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.021 0.010 199.1 -91: (ns/day) (hour/ns) -91: Performance: 142.471 0.168 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 -91: -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.032 0.016 199.5 -91: (ns/day) (hour/ns) -91: Performance: 91.716 0.262 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (327 ms) -91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (15643 ms total) -91: -91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest -91: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'FirstWaterMolecule' has 3 atoms -91: Pull group 2 'SecondWaterMolecule' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 9.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: NVE simulation: will use the initial temperature of 2573.591 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 1.112 nm 1.000 nm -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 3 of the 3 non-bonded parameter combinations -91: -91: Generated 3 of the 3 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.206 0.103 199.9 -91: (ns/day) (hour/ns) -91: Performance: 14.268 1.682 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.114 0.057 199.7 -91: (ns/day) (hour/ns) -91: Performance: 25.624 0.937 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (192 ms) -91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (192 ms total) -91: -91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest -91: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -91: that with the Verlet scheme, nstlist has no effect on the accuracy of -91: your simulation. -91: -91: -91: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: Setting nstcalcenergy (100) equal to nstenergy (4) -91: -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'FirstWaterMolecule' has 3 atoms -91: Pull group 2 'SecondWaterMolecule' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 9.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: -91: NVE simulation: will use the initial temperature of 2573.591 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 1.112 nm 1.000 nm -91: -91: There were 3 NOTEs -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: Generated 3 of the 3 non-bonded parameter combinations -91: -91: Generated 3 of the 3 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.204 0.102 199.9 -91: (ns/day) (hour/ns) -91: Performance: 14.355 1.672 -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI thread -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 16 steps, 0.0 ps. -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.205 0.102 199.9 -91: (ns/day) (hour/ns) -91: Performance: 14.354 1.672 -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file -91: Opened /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -91: -91: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (221 ms) -91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (221 ms total) -91: -91: [----------] Global test environment tear-down -91: [==========] 94 tests from 4 test suites ran. (36755 ms total) -91: [ PASSED ] 94 tests. -91/92 Test #91: MdrunSimulatorComparison .................. Passed 36.77 sec -test 92 - Start 92: MdrunVirtualSiteTests - -92: Test command: /build/reproducible-path/gromacs-2025.3/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" -92: Working Directory: /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests -92: Test timeout computed to be: 600 -92: [==========] Running 37 tests from 2 test suites. -92: [----------] Global test environment set-up. -92: [----------] 1 test from VirtualSiteVelocityTest -92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect -92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) -92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) -92: -92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 8.0%. -92: The balanceable part of the MD step is 29%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 2.3%. -92: -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 2.036 1.018 200.0 -92: (ns/day) (hour/ns) -92: Performance: 0.764 31.425 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: trr version: GMX_trn_file (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (1073 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 8.0%. -92: The balanceable part of the MD step is 38%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 3.1%. -92: -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 2.398 1.199 200.0 -92: (ns/day) (hour/ns) -92: Performance: 0.648 37.010 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (1380 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 1.6%. -92: The balanceable part of the MD step is 35%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.6%. -92: -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 3.548 1.774 200.0 -92: (ns/day) (hour/ns) -92: Performance: 0.438 54.754 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (1805 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 2.989 1.494 200.0 -92: (ns/day) (hour/ns) -92: Performance: 0.520 46.125 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (1542 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.067 0.034 199.5 -92: (ns/day) (hour/ns) -92: Performance: 23.163 1.036 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (54 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.047 0.024 199.5 -92: (ns/day) (hour/ns) -92: Performance: 32.981 0.728 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (41 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.051 0.026 199.6 -92: (ns/day) (hour/ns) -92: Performance: 30.195 0.795 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (55 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 48 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.035 0.018 199.3 -92: (ns/day) (hour/ns) -92: Performance: 44.312 0.542 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (30 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -92: 1 -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 5 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.821 0.411 200.0 -92: (ns/day) (hour/ns) -92: Performance: 1.894 12.671 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (536 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 2.0%. -92: The balanceable part of the MD step is 28%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.6%. -92: -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.069 0.035 199.7 -92: (ns/day) (hour/ns) -92: Performance: 22.437 1.070 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (44 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: -92: Dynamic load balancing report: -92: DLB was off during the run due to low measured imbalance. -92: Average load imbalance: 1.7%. -92: The balanceable part of the MD step is 41%, load imbalance is computed from this. -92: Part of the total run time spent waiting due to load imbalance: 0.7%. -92: -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 3.009 1.505 200.0 -92: (ns/day) (hour/ns) -92: Performance: 0.517 46.436 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (1583 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.972 0.486 200.0 -92: (ns/day) (hour/ns) -92: Performance: 1.600 15.001 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (507 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.518 0.259 199.9 -92: (ns/day) (hour/ns) -92: Performance: 2.999 8.003 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (286 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.068 0.034 199.7 -92: (ns/day) (hour/ns) -92: Performance: 22.962 1.045 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (45 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 47 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.019 0.009 198.9 -92: (ns/day) (hour/ns) -92: Performance: 83.080 0.289 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (22 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 50 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.188 0.094 199.8 -92: (ns/day) (hour/ns) -92: Performance: 8.262 2.905 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (210 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.064 0.032 199.6 -92: (ns/day) (hour/ns) -92: Performance: 24.384 0.984 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (44 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 48 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.032 0.016 199.3 -92: (ns/day) (hour/ns) -92: Performance: 47.940 0.501 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (41 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 46 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.027 0.013 199.1 -92: (ns/day) (hour/ns) -92: Performance: 58.207 0.412 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (29 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 49 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.046 0.023 199.4 -92: (ns/day) (hour/ns) -92: Performance: 34.006 0.706 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (39 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: Setting nstcalcenergy (100) equal to nstenergy (4) -92: -92: Number of degrees of freedom in T-Coupling group System is 45.00 -92: -92: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: There are 6 non-linear virtual site constructions. Their contribution to -92: the energy error is approximated. In most cases this does not affect the -92: error significantly. -92: -92: -92: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -92: You are using a plain Coulomb cut-off, which might produce artifacts. -92: You might want to consider using PME electrostatics. -92: -92: -92: -92: There were 4 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 -92: -92: Update groups can not be used for this system because an incompatible virtual site type is used -92: -92: Using 2 MPI threads -92: Using 1 OpenMP thread per tMPI thread -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Virtual sites test system in vacuo' -92: 8 steps, 0.0 ps. -92: Generated 3 of the 6 non-bonded parameter combinations -92: -92: Excluding 3 bonded neighbours molecule type 'VSTEST' -92: -92: Cleaning up constraints and constant bonded interactions with virtual sites -92: -92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -92: -92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -92: -92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -92: -92: Note that mdrun will redetermine rlist based on the actual pair-list setup -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: NOTE: 47 % of the run time was spent communicating energies, -92: you might want to increase some nst* mdp options -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.022 0.011 198.4 -92: (ns/day) (hour/ns) -92: Performance: 69.996 0.343 -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: Reading file /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (double precision) -92: -92: Reading virtual site types... -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (27 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) -92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 -92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) -92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (9405 ms total) -92: -92: [----------] Global test environment tear-down -92: [==========] 37 tests from 2 test suites ran. (9431 ms total) -92: [ PASSED ] 37 tests. -92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 9.45 sec - -100% tests passed, 0 tests failed out of 92 - -Label Time Summary: -GTest = 591.55 sec*proc (90 tests) -IntegrationTest = 390.82 sec*proc (29 tests) -MpiTest = 222.05 sec*proc (21 tests) -QuickGpuTest = 155.06 sec*proc (23 tests) -SlowGpuTest = 366.23 sec*proc (14 tests) -SlowTest = 178.00 sec*proc (14 tests) -UnitTest = 22.73 sec*proc (47 tests) - -Total Test time (real) = 340.80 sec touch build-basic dh_testdir -LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/mpi/lib /usr/bin/make -j40 -C build/mpi +LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/mpi/lib /usr/bin/make -j42 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 @@ -222006,171 +5287,171 @@ /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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/build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/eigensolver.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_float.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwlzh.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/gmx_arpack.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/sparsematrix.cpp +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/coder.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractoption.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/lock.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsection.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/src/gromacs/options/filenameoptionmanager.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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'/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsvisitor.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/merge_sort.c -[ 2%] Built target thread_mpi -[ 2%] Built target internal_rpc_xdr +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_meta.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/timeunitmanager.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsassigner.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_opes.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/treesupport.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/mtf.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_restraint.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/rle.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/vals16.c +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsection.cpp +[ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/warnmalloc.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c +[ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_alchlambda.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_angles.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/md5.c -[ 4%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_combination.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_coordnums.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/timeunitmanager.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_distances.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_gpath.cpp +[ 4%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_protein.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_rotations.cpp -[ 4%] Built target lmfit_objlib -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_volmaps.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' [ 4%] Built target energyanalysis +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvardeps.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +[ 4%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarmodule.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +[ 4%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparse.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 4%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_replicas.cpp @@ -222252,9 +5533,9 @@ make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' [ 8%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 13%] Built target colvars_objlib +[ 8%] Built target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 13%] Built target taskassignment +[ 13%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend @@ -223086,44 +6367,44 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/resourceassignment.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include 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/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tpr.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tpr.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/transformations.cpp @@ -223141,12 +6422,12 @@ /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -MF CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o.d -o CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp/sessionresources.cpp @@ -223176,13 +6457,13 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp/nullpotential.cpp -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o @@ -223224,25 +6505,25 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build -/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/argon-forces-integration.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 +cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.3/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' [100%] Built target argon-forces-integration -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.3/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -j40 -C build/mpi-dp +/usr/bin/make -j42 -C build/mpi-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.3/build/mpi-dp//CMakeFiles/progress.marks @@ -223265,9 +6546,9 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend @@ -223275,152 +6556,152 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr.cpp -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/tmpi_malloc.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_stdio.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_array.cpp +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c 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'/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwlzh.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/atomic.cpp -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwt.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/lock.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_float.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/eigensolver.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/atomic.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr_stdio.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/bwt.c +/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvar.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra/gmx_arpack.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractoption.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/energyterm.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/pthreads.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/lock.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractoption.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/huffmem.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' [ 0%] Built target release-version-info -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c 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/usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_abmd.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/options.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/mtf.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsassigner.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsection.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/tng_compress.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_alb.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c 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-Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/timeunitmanager.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 0%] Built target thread_mpi -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o 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/build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/vals16.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/warnmalloc.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/treesupport.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/tng_io.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/mtf.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_alb.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_meta.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/rle.c +[ 0%] Built target internal_rpc_xdr +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/tng_compress.c +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_opes.cpp +[ 0%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_coordnums.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_distances.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_neuralnetwork.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/widemuldiv.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_protein.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_rotations.cpp +[ 0%] Built target gmx_objlib +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/xtc3.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/tng_io.c +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvardeps.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvargrid.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarmodule.cpp -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' [ 0%] Built target energyanalysis +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparams.cpp -[ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarparse.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +[ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_replicas.cpp +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_system.cpp +[ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvars_memstream.cpp @@ -223458,23 +6739,23 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidegpuusage.cpp +/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidesimulationworkload.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/findallgputasks.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/reportgpuusage.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/resourcedivision.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. 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-I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/expandedensembleelement.cpp @@ -224332,47 +7613,47 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/resourceassignment.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/context.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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-Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/topology.cpp 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/transformations.cpp +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/util/setup.cpp @@ -224414,111219 +7695,6 @@ make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/mpi/lib /usr/bin/make -j40 -C build/mpi tests -make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/VerifyGlobs.cmake -/usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 -/usr/bin/make -f CMakeFiles/Makefile2 tests -make[2]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/VerifyGlobs.cmake -/usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles 75 -/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend -/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" 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src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 9%] Built target modularsimulator -/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs 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/build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build -/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 60%] Built target gmxapi -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend -[ 60%] Built target gmx -[ 61%] Built target nblib -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend -/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend -/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.top -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build -/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 61%] Built target methane-water-integration -[ 61%] Built target gmxapi_extension_resources -[ 61%] Built target argon-forces-integration -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" -Generating 1-4 interactions: fudge = 0.5 -Number of degrees of freedom in T-Coupling group rest is 9.00 -The integrator does not provide a ensemble temperature, there is no system ensemble temperature - -NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: - NVE simulation: will use the initial temperature of 2573.591 K for - determining the Verlet buffer size - - -NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: - You are using a plain Coulomb cut-off, which might produce artifacts. - You might want to consider using PME electrostatics. - - - -There were 2 NOTEs -Setting the LD random seed to -120784461 - -Generated 3 of the 3 non-bonded parameter combinations - -Generated 3 of the 3 1-4 parameter combinations - -Excluding 2 bonded neighbours molecule type 'SOL' - -Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -Analysing residue names: -There are: 2 Water residues - -Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K - -Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm - -Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm - -Note that mdrun will redetermine rlist based on the actual pair-list setup - -This run will generate roughly 0 Mb of data -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 61%] Built target gmxapi_extension_spc2_water_box -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 61%] Built target gmxapi_extension_ensemblepotential -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 -/usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 61%] Built target gtest -/usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend -/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build -/usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/src/gmock-all.cc -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/src/gtest_main.cc -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 -/usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest_main.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest_main.so.1.13.0 -o ../../../../lib/libgtest_main.so.1.13.0 CMakeFiles/gtest_main.dir/src/gtest_main.cc.o ../../../../lib/libgtest.so.1.13.0 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 61%] Built target gtest_main -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build -/usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/tests/test_histogram.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend -/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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'/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/tests/com.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 64%] Built target timing-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include 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directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 66%] Built target nnpot_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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/usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 66%] Built target table-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c 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directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 68%] Built target testutils-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 68%] Built target pbcutil-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/listoflists.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/tests/option.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/tests/device_management.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 68%] Built target qmmm_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/random/tests/uniformintdistribution.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 68%] Built target mdspan-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest 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directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 69%] Built target listed_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp -[ 70%] Built target density_fitting_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/awh/tests/biassharing.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c 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directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 72%] Built target topology-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/expanded.cpp -[ 73%] Built target nbnxm-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -[ 74%] Built target colvars_applied_forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/math/tests/matrix.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 76%] Built target mdtypes-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/message_string_collector.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 76%] Built target gmxana-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection 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'/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/multisimtest.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem 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CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/replicaexchange_equivalence.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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target mdrun-output-test -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include 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"CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 84%] Built target mdrun-single-rank-algorithms-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/tests/pull_rotation.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem 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CMakeFiles/utility-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 85%] Built target mdrun-tpi-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/status.cpp -cd 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests/version.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d 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api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" -[ 85%] Built target mdrun-io-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/workflow/tests/workflow.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem 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"CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 89%] Built target mdrun-non-integrator-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/nbkernelsystem.cpp -/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/util/tests /build/reproducible-path/gromacs-2025.3/build/mpi 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'/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/util/tests/setup.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 90%] Built target workflow-details-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/util/tests/traits.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/tests/simstate.cpp -[ 92%] Built target mdrun-mpi-pme-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 92%] Built target mdrun-multisim-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp -[ 92%] Built target mdrun-multisim-replex-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/helpers.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src 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'/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include 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Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" -[ 92%] Built target workflow-details-mpi-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest 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'/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/api/nblib/tests -I/build/reproducible-path/gromacs-2025.3/api/nblib/include -I/build/reproducible-path/gromacs-2025.3/api/nblib -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.3/api/nblib/listed_forces/tests/transformations.cpp -[ 93%] Built target mdrun-coordination-coupling-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/analysisdata/tests/lifetime.cpp -[ 93%] Built target mdrun-coordination-basic-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/commandline/tests/filenm.cpp -cd 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-I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend -[ 93%] Built target selection-test -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 93%] Built target mdrun-rotation-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 93%] Built target mdrun-vsites-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include 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/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 93%] Built target mdrun-simulator-comparison-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection 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-I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/unionfind.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target mdrunutility-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/testutils/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/testutils/unittest_main.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target nblib-integrator-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 -[ 94%] Built target onlinehelp-test -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target mdrun-fep-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target plumed_md-test -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target mdrun-multisim-replex-equivalence-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target mdrun-pull-test -[ 94%] Built target commandline-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 94%] Built target analysisdata-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 96%] Built target nblib-setup-test -/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 96%] Built target nblib-tests -cd /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 96%] Built target nblib-listed-forces-test -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 -cd /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 98%] Built target trajectoryanalysis-test -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[100%] Built target math-test -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[100%] Built target tests -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles 0 -make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -(cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.3/build/mpi/lib \ - OMPI_MCA_rmaps_base_oversubscribe=1 \ - PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ - ctest -V) -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/mpi/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/mpi/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.3/build/mpi/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/gromacs-2025.3/build/mpi/DartConfiguration.tcl -Test project /build/reproducible-path/gromacs-2025.3/build/mpi -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -test 1 - Start 1: GmxapiExternalInterfaceTests - -1: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" -1: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests -1: Test timeout computed to be: 600 -1: [==========] Running 9 tests from 1 test suite. -1: [----------] Global test environment set-up. -1: [----------] 9 tests from GmxApiTest -1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to -33702473 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.613 2.306 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.219 109.345 -1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (2797 ms) -1: [ RUN ] GmxApiTest.RunnerBasicMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to -1048883 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.632 2.316 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.219 109.813 -1: [ OK ] GmxApiTest.RunnerBasicMD (2749 ms) -1: [ RUN ] GmxApiTest.RunnerReinitialize -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: -1: Received the remote INT/TERM signal, stopping within 200 steps -1: -1: Setting the LD random seed to -201981975 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 3.658 1.829 200.0 -1: (ns/day) (hour/ns) -1: Performance: 1.938 12.387 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 20 steps, 0.0 ps. -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.603 2.301 200.0 -1: (ns/day) (hour/ns) -1: Performance: 1.540 15.586 -1: [ OK ] GmxApiTest.RunnerReinitialize (4661 ms) -1: [ RUN ] GmxApiTest.RunnerChainedMD -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 2 steps, 0.0 ps. -1: Setting the LD random seed to -34162193 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 4.046 2.023 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.250 95.912 -1: trr version: GMX_trn_file (single precision) -1: -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Setting nsteps to 4 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -1: Input file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 2 -1: Runtime for the run 0.00390625 ps -1: Run end step 2 -1: Run end time 0.00390625 ps -1: -1: -1: Output file: -1: Run start step 0 -1: Run start time 0 ps -1: Step to be made during run 4 -1: Runtime for the run 0.0078125 ps -1: Run end step 4 -1: Run end time 0.0078125 ps -1: -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 1.191 0.595 200.0 -1: (ns/day) (hour/ns) -1: Performance: 0.850 28.230 -1: -1: [ OK ] GmxApiTest.RunnerChainedMD (3060 ms) -1: [ RUN ] GmxApiTest.Status -1: [ OK ] GmxApiTest.Status (0 ms) -1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: Setting the LD random seed to -542777417 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: -1: Writing final coordinates. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 0.050 0.025 199.3 -1: (ns/day) (hour/ns) -1: Performance: 33.378 0.719 -1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -1: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps -1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -1: -1: -1: Using 1 MPI process -1: Using 2 OpenMP threads -1: -1: -1: NOTE: The number of threads is not equal to the number of (logical) cpus -1: and the -pin option is set to auto: will not pin threads to cpus. -1: This can lead to significant performance degradation. -1: Consider using -pin on (and -pinoffset in case you run multiple jobs). -1: starting mdrun 'Water and methane' -1: 4 steps, 0.0 ps. -1: -1: Core t (s) Wall t (s) (%) -1: Time: 0.028 0.014 199.1 -1: (ns/day) (hour/ns) -1: Performance: 23.748 1.011 -1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (363 ms) -1: [ RUN ] GmxApiTest.SystemConstruction -1: Generating 1-4 interactions: fudge = 0.5 -1: -1: NOTE 1 [file spc_and_methane.top, line 33]: -1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -1: the time step of 2.0e-03 ps. -1: Maybe you forgot to change the constraints mdp option. -1: -1: Number of degrees of freedom in T-Coupling group System is 18.00 -1: -1: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: -1: You are using a plain Coulomb cut-off, which might produce artifacts. -1: You might want to consider using PME electrostatics. -1: -1: -1: -1: There were 2 NOTEs -1: Setting the LD random seed to -78651466 -1: -1: Generated 331705 of the 331705 non-bonded parameter combinations -1: -1: Generated 331705 of the 331705 1-4 parameter combinations -1: -1: Excluding 2 bonded neighbours molecule type 'SOL' -1: -1: Excluding 3 bonded neighbours molecule type 'methane' -1: -1: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -1: -1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -1: -1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -1: -1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -1: -1: Note that mdrun will redetermine rlist based on the actual pair-list setup -1: -1: This run will generate roughly 0 Mb of data -1: [ OK ] GmxApiTest.SystemConstruction (223 ms) -1: [ RUN ] GmxApiTest.SaneVersionComparisons -1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) -1: [ RUN ] GmxApiTest.VersionNamed0_1_Features -1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) -1: [----------] 9 tests from GmxApiTest (13856 ms total) -1: -1: [----------] Global test environment tear-down -1: [==========] 9 tests from 1 test suite ran. (13893 ms total) -1: [ PASSED ] 9 tests. - 1/96 Test #1: GmxapiExternalInterfaceTests ................. Passed 14.36 sec -test 2 - Start 2: GmxapiMpiTests - -2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" -2: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests -2: Test timeout computed to be: 600 -2: [==========] Running 13 tests from 1 test suite. -2: [----------] Global test environment set-up. -2: [----------] 13 tests from GmxApiTest -2: [ RUN ] GmxApiTest.AllContext -2: [ OK ] GmxApiTest.AllContext (133 ms) -2: [ RUN ] GmxApiTest.NullContext -2: [ OK ] GmxApiTest.NullContext (0 ms) -2: [ RUN ] GmxApiTest.MpiWorldContext -2: [ OK ] GmxApiTest.MpiWorldContext (30 ms) -2: [ RUN ] GmxApiTest.MpiSplitContext -2: [ OK ] GmxApiTest.MpiSplitContext (51 ms) -2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD -2: Setting the LD random seed to -39849494 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Setting the LD random seed to -4194578 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: This run will generate roughly 0 Mb of data -2: -2: There were 2 NOTEs -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 2 steps, 0.0 ps. -2: -2: Writing final coordinates. -2: -2: NOTE: 48 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.063 0.016 397.3 -2: (ns/day) (hour/ns) -2: Performance: 31.908 0.752 -2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (544 ms) -2: [ RUN ] GmxApiTest.RunnerBasicMD -2: Setting the LD random seed to -305006081 -2: Setting the LD random seed to -18515017 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 2 steps, 0.0 ps. -2: -2: Writing final coordinates. -2: -2: NOTE: 48 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.049 0.012 396.9 -2: (ns/day) (hour/ns) -2: Performance: 40.616 0.591 -2: [ OK ] GmxApiTest.RunnerBasicMD (360 ms) -2: [ RUN ] GmxApiTest.RunnerReinitialize -2: Setting the LD random seed to -2108169 -2: Setting the LD random seed to -538052121 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: This run will generate roughly 0 Mb of data -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 20 steps, 0.0 ps. -2: -2: -2: Received the remote INT/TERM signal, stopping within 200 steps -2: -2: -2: -2: Received the remote INT/TERM signal, stopping within 200 steps -2: -2: -2: Writing final coordinates. -2: -2: NOTE: 50 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.731 0.183 399.7 -2: (ns/day) (hour/ns) -2: Performance: 19.388 1.238 -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 20 steps, 0.0 ps. -2: -2: Writing final coordinates. -2: -2: NOTE: 47 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.057 0.014 397.0 -2: (ns/day) (hour/ns) -2: Performance: 246.232 0.097 -2: [ OK ] GmxApiTest.RunnerReinitialize (731 ms) -2: [ RUN ] GmxApiTest.RunnerChainedMD -2: Setting the LD random seed to -19595301 -2: Setting the LD random seed to -58220689 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: This run will generate roughly 0 Mb of data -2: -2: There were 2 NOTEs -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 2 steps, 0.0 ps. -2: -2: Writing final coordinates. -2: -2: NOTE: 50 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 12.707 3.177 400.0 -2: (ns/day) (hour/ns) -2: Performance: 0.159 150.600 -2: trr version: GMX_trn_file (single precision) -2: -2: trr version: GMX_trn_file (single precision) -2: -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Setting nsteps to 4 -2: Setting nsteps to 4 -2: Input file: -2: Run start step 0 -2: Run start time 0 ps -2: Step to be made during run 2 -2: Runtime for the run 0.00390625 ps -2: Run end step 2 -2: Run end time 0.00390625 ps -2: -2: -2: Output file: -2: Run start step 0 -2: Run start time 0 ps -2: Step to be made during run 4 -2: Runtime for the run 0.0078125 ps -2: Run end step 4 -2: Run end time 0.0078125 ps -2: -2: Input file: -2: Run start step 0 -2: Run start time 0 ps -2: Step to be made during run 2 -2: Runtime for the run 0.00390625 ps -2: Run end step 2 -2: Run end time 0.00390625 ps -2: -2: -2: Output file: -2: Run start step 0 -2: Run start time 0 ps -2: Step to be made during run 4 -2: Runtime for the run 0.0078125 ps -2: Run end step 4 -2: Run end time 0.0078125 ps -2: -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -2: -2: Writing final coordinates. -2: -2: NOTE: 50 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.661 0.165 399.8 -2: (ns/day) (hour/ns) -2: Performance: 3.064 7.834 -2: -2: -2: [ OK ] GmxApiTest.RunnerChainedMD (3616 ms) -2: [ RUN ] GmxApiTest.Status -2: [ OK ] GmxApiTest.Status (0 ms) -2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient -2: Setting the LD random seed to 2140782494 -2: Setting the LD random seed to -151015681 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: There were 2 NOTEs -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 4 steps, 0.0 ps. -2: -2: Writing final coordinates. -2: -2: -2: Dynamic load balancing report: -2: DLB was off during the run due to low measured imbalance. -2: Average load imbalance: 19.6%. -2: The balanceable part of the MD step is 3%, load imbalance is computed from this. -2: Part of the total run time spent waiting due to load imbalance: 0.6%. -2: -2: -2: NOTE: 46 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.052 0.013 397.8 -2: (ns/day) (hour/ns) -2: Performance: 64.895 0.370 -2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -2: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps -2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 -2: -2: -2: Using 2 MPI processes -2: Using 2 OpenMP threads per MPI process -2: -2: -2: NOTE: The number of threads is not equal to the number of (logical) cpus -2: and the -pin option is set to auto: will not pin threads to cpus. -2: This can lead to significant performance degradation. -2: Consider using -pin on (and -pinoffset in case you run multiple jobs). -2: starting mdrun 'Water and methane' -2: 4 steps, 0.0 ps. -2: -2: -2: Dynamic load balancing report: -2: DLB was off during the run due to low measured imbalance. -2: Average load imbalance: 9.5%. -2: The balanceable part of the MD step is 9%, load imbalance is computed from this. -2: Part of the total run time spent waiting due to load imbalance: 0.8%. -2: -2: -2: NOTE: 48 % of the run time was spent communicating energies, -2: you might want to increase some nst* mdp options -2: -2: Core t (s) Wall t (s) (%) -2: Time: 0.043 0.011 397.2 -2: (ns/day) (hour/ns) -2: Performance: 31.057 0.773 -2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (317 ms) -2: [ RUN ] GmxApiTest.SystemConstruction -2: Setting the LD random seed to -1117375517 -2: Setting the LD random seed to 2146957311 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 non-bonded parameter combinations -2: Generating 1-4 interactions: fudge = 0.5 -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: -2: Generated 331705 of the 331705 1-4 parameter combinations -2: -2: Excluding 2 bonded neighbours molecule type 'SOL' -2: -2: Excluding 3 bonded neighbours molecule type 'methane' -2: -2: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -2: -2: NOTE 1 [file spc_and_methane.top, line 33]: -2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -2: the time step of 2.0e-03 ps. -2: Maybe you forgot to change the constraints mdp option. -2: -2: Number of degrees of freedom in T-Coupling group System is 18.00 -2: -2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -2: -2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -2: -2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -2: -2: Note that mdrun will redetermine rlist based on the actual pair-list setup -2: -2: This run will generate roughly 0 Mb of data -2: -2: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: -2: You are using a plain Coulomb cut-off, which might produce artifacts. -2: You might want to consider using PME electrostatics. -2: -2: -2: -2: There were 2 NOTEs -2: [ OK ] GmxApiTest.SystemConstruction (237 ms) -2: [ RUN ] GmxApiTest.SaneVersionComparisons -2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) -2: [ RUN ] GmxApiTest.VersionNamed0_1_Features -2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) -2: [----------] 13 tests from GmxApiTest (6029 ms total) -2: -2: [----------] Global test environment tear-down -2: [==========] 13 tests from 1 test suite ran. (6067 ms total) -2: [ PASSED ] 13 tests. - 2/96 Test #2: GmxapiMpiTests ............................... Passed 6.35 sec -test 3 - Start 3: GmxapiInternalInterfaceTests - -3: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" -3: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests -3: Test timeout computed to be: 600 -3: [==========] Running 2 tests from 1 test suite. -3: [----------] Global test environment set-up. -3: [----------] 2 tests from GmxApiTest -3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl -3: Generating 1-4 interactions: fudge = 0.5 -3: -3: NOTE 1 [file spc_and_methane.top, line 33]: -3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -3: the time step of 2.0e-03 ps. -3: Maybe you forgot to change the constraints mdp option. -3: -3: Number of degrees of freedom in T-Coupling group System is 18.00 -3: -3: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: -3: You are using a plain Coulomb cut-off, which might produce artifacts. -3: You might want to consider using PME electrostatics. -3: -3: -3: -3: There were 2 NOTEs -3: Setting the LD random seed to -1613758466 -3: -3: Generated 331705 of the 331705 non-bonded parameter combinations -3: -3: Generated 331705 of the 331705 1-4 parameter combinations -3: -3: Excluding 2 bonded neighbours molecule type 'SOL' -3: -3: Excluding 3 bonded neighbours molecule type 'methane' -3: -3: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -3: -3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -3: -3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -3: -3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -3: -3: Note that mdrun will redetermine rlist based on the actual pair-list setup -3: -3: This run will generate roughly 0 Mb of data -3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (226 ms) -3: [ RUN ] GmxApiTest.CreateApiWorkflow -3: Generating 1-4 interactions: fudge = 0.5 -3: -3: NOTE 1 [file spc_and_methane.top, line 33]: -3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -3: the time step of 2.0e-03 ps. -3: Maybe you forgot to change the constraints mdp option. -3: -3: Number of degrees of freedom in T-Coupling group System is 18.00 -3: -3: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: -3: You are using a plain Coulomb cut-off, which might produce artifacts. -3: You might want to consider using PME electrostatics. -3: -3: -3: -3: There were 2 NOTEs -3: Setting the LD random seed to -1073965313 -3: -3: Generated 331705 of the 331705 non-bonded parameter combinations -3: -3: Generated 331705 of the 331705 1-4 parameter combinations -3: -3: Excluding 2 bonded neighbours molecule type 'SOL' -3: -3: Excluding 3 bonded neighbours molecule type 'methane' -3: -3: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -3: -3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -3: -3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -3: -3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -3: -3: Note that mdrun will redetermine rlist based on the actual pair-list setup -3: -3: This run will generate roughly 0 Mb of data -3: [ OK ] GmxApiTest.CreateApiWorkflow (338 ms) -3: [----------] 2 tests from GmxApiTest (565 ms total) -3: -3: [----------] Global test environment tear-down -3: [==========] 2 tests from 1 test suite ran. (592 ms total) -3: [ PASSED ] 2 tests. - 3/96 Test #3: GmxapiInternalInterfaceTests ................. Passed 0.79 sec -test 4 - Start 4: GmxapiInternalsMpiTests - -4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" -4: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests -4: Test timeout computed to be: 600 -4: [==========] Running 2 tests from 1 test suite. -4: [----------] Global test environment set-up. -4: [----------] 2 tests from GmxApiTest -4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl -4: Setting the LD random seed to -539101233 -4: Setting the LD random seed to -5898321 -4: -4: Generated 331705 of the 331705 non-bonded parameter combinations -4: Generating 1-4 interactions: fudge = 0.5 -4: -4: Generated 331705 of the 331705 non-bonded parameter combinations -4: Generating 1-4 interactions: fudge = 0.5 -4: -4: Generated 331705 of the 331705 1-4 parameter combinations -4: -4: Excluding 2 bonded neighbours molecule type 'SOL' -4: -4: Excluding 3 bonded neighbours molecule type 'methane' -4: -4: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -4: -4: Generated 331705 of the 331705 1-4 parameter combinations -4: -4: Excluding 2 bonded neighbours molecule type 'SOL' -4: -4: Excluding 3 bonded neighbours molecule type 'methane' -4: -4: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -4: -4: NOTE 1 [file spc_and_methane.top, line 33]: -4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -4: the time step of 2.0e-03 ps. -4: Maybe you forgot to change the constraints mdp option. -4: -4: Number of degrees of freedom in T-Coupling group System is 18.00 -4: -4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -4: -4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -4: -4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -4: -4: Note that mdrun will redetermine rlist based on the actual pair-list setup -4: -4: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: -4: You are using a plain Coulomb cut-off, which might produce artifacts. -4: You might want to consider using PME electrostatics. -4: -4: -4: -4: This run will generate roughly 0 Mb of data -4: -4: There were 2 NOTEs -4: -4: NOTE 1 [file spc_and_methane.top, line 33]: -4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -4: the time step of 2.0e-03 ps. -4: Maybe you forgot to change the constraints mdp option. -4: -4: Number of degrees of freedom in T-Coupling group System is 18.00 -4: -4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -4: -4: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: -4: You are using a plain Coulomb cut-off, which might produce artifacts. -4: You might want to consider using PME electrostatics. -4: -4: -4: -4: There were 2 NOTEs -4: -4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -4: -4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -4: -4: Note that mdrun will redetermine rlist based on the actual pair-list setup -4: -4: This run will generate roughly 0 Mb of data -4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (657 ms) -4: [ RUN ] GmxApiTest.CreateApiWorkflow -4: Setting the LD random seed to -437478497 -4: Setting the LD random seed to -892338689 -4: -4: Generated 331705 of the 331705 non-bonded parameter combinations -4: Generating 1-4 interactions: fudge = 0.5 -4: -4: Generated 331705 of the 331705 non-bonded parameter combinations -4: Generating 1-4 interactions: fudge = 0.5 -4: -4: Generated 331705 of the 331705 1-4 parameter combinations -4: -4: Excluding 2 bonded neighbours molecule type 'SOL' -4: -4: Excluding 3 bonded neighbours molecule type 'methane' -4: -4: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -4: -4: Generated 331705 of the 331705 1-4 parameter combinations -4: -4: Excluding 2 bonded neighbours molecule type 'SOL' -4: -4: Excluding 3 bonded neighbours molecule type 'methane' -4: -4: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -4: -4: NOTE 1 [file spc_and_methane.top, line 33]: -4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -4: the time step of 2.0e-03 ps. -4: Maybe you forgot to change the constraints mdp option. -4: -4: Number of degrees of freedom in T-Coupling group System is 18.00 -4: -4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -4: -4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -4: -4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -4: -4: Note that mdrun will redetermine rlist based on the actual pair-list setup -4: -4: This run will generate roughly 0 Mb of data -4: -4: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: -4: You are using a plain Coulomb cut-off, which might produce artifacts. -4: You might want to consider using PME electrostatics. -4: -4: -4: -4: There were 2 NOTEs -4: -4: NOTE 1 [file spc_and_methane.top, line 33]: -4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an -4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times -4: the time step of 2.0e-03 ps. -4: Maybe you forgot to change the constraints mdp option. -4: -4: Number of degrees of freedom in T-Coupling group System is 18.00 -4: -4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -4: -4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm -4: -4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm -4: -4: Note that mdrun will redetermine rlist based on the actual pair-list setup -4: -4: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: -4: You are using a plain Coulomb cut-off, which might produce artifacts. -4: You might want to consider using PME electrostatics. -4: -4: -4: -4: There were 2 NOTEs -4: -4: This run will generate roughly 0 Mb of data -4: [ OK ] GmxApiTest.CreateApiWorkflow (221 ms) -4: [----------] 2 tests from GmxApiTest (879 ms total) -4: -4: [----------] Global test environment tear-down -4: [==========] 2 tests from 1 test suite ran. (912 ms total) -4: [ PASSED ] 2 tests. - 4/96 Test #4: GmxapiInternalsMpiTests ...................... Passed 1.38 sec -test 5 - Start 5: NbLibListedForcesTests - -5: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" -5: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/listed_forces/tests -5: Test timeout computed to be: 600 -5: [==========] Running 44 tests from 22 test suites. -5: [----------] Global test environment set-up. -5: [----------] 8 tests from NBlibTest -5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks -5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) -5: [ RUN ] NBlibTest.BondTypesLessThanWorks -5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) -5: [ RUN ] NBlibTest.CanSplitListedWork -5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) -5: [ RUN ] NBlibTest.ListedForceBuffer -5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) -5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct -5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) -5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes -5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) -5: [ RUN ] NBlibTest.EndToEndListedComparison -5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) -5: [ RUN ] NBlibTest.shiftForcesAreCorrect -5: [ OK ] NBlibTest.shiftForcesAreCorrect (13 ms) -5: [----------] 8 tests from NBlibTest (14 ms total) -5: -5: [----------] 1 test from Kernels -5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute -5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) -5: [----------] 1 test from Kernels (0 ms total) -5: -5: [----------] 1 test from FourCenter -5: [ RUN ] FourCenter.ListedForcesProperDihedralTest -5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) -5: [----------] 1 test from FourCenter (0 ms total) -5: -5: [----------] 7 tests from ThreeCenter -5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest -5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest -5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest -5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest -5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest -5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest -5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) -5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest -5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) -5: [----------] 7 tests from ThreeCenter (0 ms total) -5: -5: [----------] 5 tests from TwoCenter -5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest -5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) -5: [ RUN ] TwoCenter.ListedForcesG96BondTest -5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) -5: [ RUN ] TwoCenter.ListedForcesCubicBondTest -5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) -5: [ RUN ] TwoCenter.ListedForcesMorseBondTest -5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) -5: [ RUN ] TwoCenter.ListedForcesFeneBondTest -5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) -5: [----------] 5 tests from TwoCenter (0 ms total) -5: -5: [----------] 5 tests from ListedExampleData -5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces -5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) -5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies -5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) -5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces -5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) -5: [ RUN ] ListedExampleData.CanReduceForces -5: [ OK ] ListedExampleData.CanReduceForces (0 ms) -5: [ RUN ] ListedExampleData.CanReduceEnergies -5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) -5: [----------] 5 tests from ListedExampleData (0 ms total) -5: -5: [----------] 1 test from LinearChainDataFixture -5: [ RUN ] LinearChainDataFixture.Multithreading -5: [ OK ] LinearChainDataFixture.Multithreading (0 ms) -5: [----------] 1 test from LinearChainDataFixture (0 ms total) -5: -5: [----------] 2 tests from ListedShims -5: [ RUN ] ListedShims.ParameterConversion -5: [ OK ] ListedShims.ParameterConversion (0 ms) -5: [ RUN ] ListedShims.GmxToNblibConversion -5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) -5: [----------] 2 tests from ListedShims (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) -5: -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral -5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth -5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) -5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) -5: -5: [----------] 1 test from ListedTransformations -5: [ RUN ] ListedTransformations.SortInteractionIndices -5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) -5: [----------] 1 test from ListedTransformations (0 ms total) -5: -5: [----------] Global test environment tear-down -5: [==========] 44 tests from 22 test suites ran. (17 ms total) -5: [ PASSED ] 44 tests. - 5/96 Test #5: NbLibListedForcesTests ....................... Passed 0.21 sec -test 6 - Start 6: NbLibSamplesTestArgon - -6: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/argon-forces-integration -6: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples -6: Test timeout computed to be: 1500 -6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 -6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 -6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 -6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 - 6/96 Test #6: NbLibSamplesTestArgon ........................ Passed 0.16 sec -test 7 - Start 7: NbLibSamplesTestMethaneWater - -7: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/methane-water-integration -7: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/samples -7: Test timeout computed to be: 1500 -7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 -7: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 - 7/96 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.16 sec -test 8 - Start 8: NbLibUtilTests - -8: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibUtilTests.xml" -8: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/util/tests -8: Test timeout computed to be: 30 -8: [==========] Running 16 tests from 2 test suites. -8: [----------] Global test environment set-up. -8: [----------] 6 tests from NBlibTest -8: [ RUN ] NBlibTest.isRealValued -8: [ OK ] NBlibTest.isRealValued (0 ms) -8: [ RUN ] NBlibTest.checkNumericValuesHasNan -8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) -8: [ RUN ] NBlibTest.checkNumericValuesHasInf -8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) -8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect -8: Velocities were taken from a Maxwell distribution at 300 K -8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) -8: [ RUN ] NBlibTest.generateVelocitySize -8: Velocities were taken from a Maxwell distribution at 300 K -8: [ OK ] NBlibTest.generateVelocitySize (0 ms) -8: [ RUN ] NBlibTest.generateVelocityCheckNumbers -8: Velocities were taken from a Maxwell distribution at 300 K -8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) -8: [----------] 6 tests from NBlibTest (0 ms total) -8: -8: [----------] 10 tests from NblibTraitsUtils -8: [ RUN ] NblibTraitsUtils.FuseTwo -8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) -8: [ RUN ] NblibTraitsUtils.Fuse -8: [ OK ] NblibTraitsUtils.Fuse (0 ms) -8: [ RUN ] NblibTraitsUtils.Repeat -8: [ OK ] NblibTraitsUtils.Repeat (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 -8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 -8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 -8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 -8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) -8: [ RUN ] NblibTraitsUtils.Contains -8: [ OK ] NblibTraitsUtils.Contains (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated -8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) -8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated -8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) -8: [----------] 10 tests from NblibTraitsUtils (0 ms total) -8: -8: [----------] Global test environment tear-down -8: [==========] 16 tests from 2 test suites ran. (0 ms total) -8: [ PASSED ] 16 tests. - 8/96 Test #8: NbLibUtilTests ............................... Passed 0.21 sec -test 9 - Start 9: NbLibSetupTests - -9: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibSetupTests.xml" -9: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests -9: Test timeout computed to be: 600 -9: [==========] Running 57 tests from 3 test suites. -9: [----------] Global test environment set-up. -9: [----------] 41 tests from NBlibTest -9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN -9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) -9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf -9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) -9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN -9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) -9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf -9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) -9: [ RUN ] NBlibTest.CubicBoxWorks -9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) -9: [ RUN ] NBlibTest.BoxEqual -9: [ OK ] NBlibTest.BoxEqual (0 ms) -9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect -9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) -9: [ RUN ] NBlibTest.CanMergeInteractions -9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) -9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed -9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) -9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed -9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) -9: [ RUN ] NBlibTest.PbcHolderWorks -9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) -9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName -9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) -9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName -9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) -9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName -9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) -9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName -9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) -9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule -9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) -9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames -9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) -9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed -9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) -9: [ RUN ] NBlibTest.AtWorks -9: [ OK ] NBlibTest.AtWorks (0 ms) -9: [ RUN ] NBlibTest.AtThrows -9: [ OK ] NBlibTest.AtThrows (0 ms) -9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass -9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) -9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass -9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) -9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName -9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) -9: [ RUN ] NBlibTest.CanAddInteractions -9: [ OK ] NBlibTest.CanAddInteractions (0 ms) -9: [ RUN ] NBlibTest.CanAddUreyBradley -9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) -9: [ RUN ] NBlibTest.TopologyHasNumParticles -9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) -9: [ RUN ] NBlibTest.TopologyHasCharges -9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) -9: [ RUN ] NBlibTest.TopologyHasMasses -9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) -9: [ RUN ] NBlibTest.TopologyHasParticleTypes -9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) -9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds -9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) -9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType -9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) -9: [ RUN ] NBlibTest.TopologyHasExclusions -9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) -9: [ RUN ] NBlibTest.TopologyHasSequencing -9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) -9: [ RUN ] NBlibTest.TopologyCanAggregateBonds -9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) -9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs -9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) -9: [ RUN ] NBlibTest.TopologySequenceIdThrows -9: No particle O-Atom in residue SOL in molecule SOL found -9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) -9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds -9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) -9: [ RUN ] NBlibTest.TopologyListedInteractions -9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) -9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes -9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) -9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows -9: No particle Iron in residue SOL in molecule SOL found -9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) -9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks -9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) -9: [----------] 41 tests from NBlibTest (2 ms total) -9: -9: [----------] 15 tests from NbnxmSetupTest -9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups -9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) -9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto -9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) -9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo -9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) -9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM -9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) -9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM -9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) -9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto -9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) -9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount -9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) -9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain -9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) -9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv -9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) -9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks -9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) -9: [ RUN ] NbnxmSetupTest.updateForcerecWorks -9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) -9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup -9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) -9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM -9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) -9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM -9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) -9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU -9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) -9: [----------] 15 tests from NbnxmSetupTest (0 ms total) -9: -9: [----------] 1 test from VirialsTest -9: [ RUN ] VirialsTest.computeVirialTensorWorks -9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) -9: [----------] 1 test from VirialsTest (0 ms total) -9: -9: [----------] Global test environment tear-down -9: [==========] 57 tests from 3 test suites ran. (2 ms total) -9: [ PASSED ] 57 tests. - 9/96 Test #9: NbLibSetupTests .............................. Passed 0.24 sec -test 10 - Start 10: NbLibTprTests - -10: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibTprTests.xml" -10: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests -10: Test timeout computed to be: 30 -10: [==========] Running 4 tests from 1 test suite. -10: [----------] Global test environment set-up. -10: [----------] 4 tests from TprReaderTest -10: [ RUN ] TprReaderTest.SimDBTprIsCreated -10: -10: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -10: that with the Verlet scheme, nstlist has no effect on the accuracy of -10: your simulation. -10: -10: -10: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -10: Setting nstcalcenergy (100) equal to nstenergy (4) -10: -10: Number of degrees of freedom in T-Coupling group System is 33.00 -10: -10: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: -10: NVE simulation: will use the initial temperature of 68.810 K for -10: determining the Verlet buffer size -10: -10: -10: There were 3 NOTEs -10: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -10: Generated 1 of the 1 non-bonded parameter combinations -10: -10: Excluding 1 bonded neighbours molecule type 'Argon' -10: -10: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -10: -10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -10: -10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -10: -10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -10: -10: Note that mdrun will redetermine rlist based on the actual pair-list setup -10: -10: This run will generate roughly 0 Mb of data -10: [ OK ] TprReaderTest.SimDBTprIsCreated (8 ms) -10: [ RUN ] TprReaderTest.Spc2Reads -10: -10: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -10: that with the Verlet scheme, nstlist has no effect on the accuracy of -10: your simulation. -10: -10: -10: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -10: Setting nstcalcenergy (100) equal to nstenergy (4) -10: -10: Generating 1-4 interactions: fudge = 0.5 -10: Number of degrees of freedom in T-Coupling group System is 9.00 -10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -10: -10: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -10: NVE simulation: will use the initial temperature of 2573.591 K for -10: determining the Verlet buffer size -10: -10: -10: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: -10: You are using a plain Coulomb cut-off, which might produce artifacts. -10: You might want to consider using PME electrostatics. -10: -10: -10: -10: There were 4 NOTEs -10: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -10: Generated 3 of the 3 non-bonded parameter combinations -10: -10: Generated 3 of the 3 1-4 parameter combinations -10: -10: Excluding 2 bonded neighbours molecule type 'SOL' -10: -10: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -10: -10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -10: -10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -10: -10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -10: -10: Note that mdrun will redetermine rlist based on the actual pair-list setup -10: -10: This run will generate roughly 0 Mb of data -10: [ OK ] TprReaderTest.Spc2Reads (6 ms) -10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect -10: -10: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -10: that with the Verlet scheme, nstlist has no effect on the accuracy of -10: your simulation. -10: -10: -10: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -10: Setting nstcalcenergy (100) equal to nstenergy (4) -10: -10: Number of degrees of freedom in T-Coupling group System is 33.00 -10: -10: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: -10: NVE simulation: will use the initial temperature of 68.810 K for -10: determining the Verlet buffer size -10: -10: -10: There were 3 NOTEs -10: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -10: Generated 1 of the 1 non-bonded parameter combinations -10: -10: Excluding 1 bonded neighbours molecule type 'Argon' -10: -10: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -10: -10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -10: -10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -10: -10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -10: -10: Note that mdrun will redetermine rlist based on the actual pair-list setup -10: -10: This run will generate roughly 0 Mb of data -10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (5 ms) -10: [ RUN ] TprReaderTest.FCfromTprDataWorks -10: -10: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -10: that with the Verlet scheme, nstlist has no effect on the accuracy of -10: your simulation. -10: -10: -10: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -10: Setting nstcalcenergy (100) equal to nstenergy (4) -10: -10: Number of degrees of freedom in T-Coupling group System is 33.00 -10: -10: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: -10: NVE simulation: will use the initial temperature of 68.810 K for -10: determining the Verlet buffer size -10: -10: -10: There were 3 NOTEs -10: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -10: Generated 1 of the 1 non-bonded parameter combinations -10: -10: Excluding 1 bonded neighbours molecule type 'Argon' -10: -10: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -10: -10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -10: -10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -10: -10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -10: -10: Note that mdrun will redetermine rlist based on the actual pair-list setup -10: -10: This run will generate roughly 0 Mb of data -10: [ OK ] TprReaderTest.FCfromTprDataWorks (5 ms) -10: [----------] 4 tests from TprReaderTest (25 ms total) -10: -10: [----------] Global test environment tear-down -10: [==========] 4 tests from 1 test suite ran. (53 ms total) -10: [ PASSED ] 4 tests. -10/96 Test #10: NbLibTprTests ................................ Passed 0.25 sec -test 11 - Start 11: NbLibIntegrationTests - -11: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" -11: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests -11: Test timeout computed to be: 600 -11: [==========] Running 20 tests from 1 test suite. -11: [----------] Global test environment set-up. -11: [----------] 20 tests from NBlibTest -11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute -11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) -11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect -11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) -11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect -11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) -11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect -11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) -11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect -11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) -11: [ RUN ] NBlibTest.ExpectedNumberOfForces -11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) -11: [ RUN ] NBlibTest.CanIntegrateSystem -11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) -11: [ RUN ] NBlibTest.UpdateChangesForces -11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) -11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect -11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) -11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect -11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) -11: [ RUN ] NBlibTest.CanConstructSimulationState -11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) -11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN -11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) -11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF -11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) -11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN -11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) -11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF -11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) -11: [ RUN ] NBlibTest.SimulationStateCanMove -11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) -11: [ RUN ] NBlibTest.SimulationStateCanAssign -11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) -11: [ RUN ] NBlibTest.SimulationStateHasBox -11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) -11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates -11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) -11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities -11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) -11: [----------] 20 tests from NBlibTest (5 ms total) -11: -11: [----------] Global test environment tear-down -11: [==========] 20 tests from 1 test suite ran. (5 ms total) -11: [ PASSED ] 20 tests. -11/96 Test #11: NbLibIntegrationTests ........................ Passed 0.19 sec -test 12 - Start 12: NbLibIntegratorTests - -12: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" -12: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/tests -12: Test timeout computed to be: 600 -12: [==========] Running 1 test from 1 test suite. -12: [----------] Global test environment set-up. -12: [----------] 1 test from NBlibTest -12: [ RUN ] NBlibTest.IntegratorWorks -12: [ OK ] NBlibTest.IntegratorWorks (0 ms) -12: [----------] 1 test from NBlibTest (0 ms total) -12: -12: [----------] Global test environment tear-down -12: [==========] 1 test from 1 test suite ran. (0 ms total) -12: [ PASSED ] 1 test. -12/96 Test #12: NbLibIntegratorTests ......................... Passed 0.21 sec -test 13 - Start 13: TestUtilsUnitTests - -13: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" -13: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/testutils/tests -13: Test timeout computed to be: 30 -13: [==========] Running 75 tests from 7 test suites. -13: [----------] Global test environment set-up. -13: [----------] 10 tests from InteractiveTestHelperTest -13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession -13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) -13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline -13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) -13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput -13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput -13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput -13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput -13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput -13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput -13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput -13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) -13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput -13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) -13: [----------] 10 tests from InteractiveTestHelperTest (3 ms total) -13: -13: [----------] 10 tests from NameOfTestFromTupleTest -13: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple -13: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction -13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable -13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction -13: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda -13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat -13: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter -13: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor -13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray -13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) -13: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters -13: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) -13: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) -13: -13: [----------] 3 tests from RefDataFilenameMakerTest -13: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction -13: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) -13: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters -13: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) -13: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty -13: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) -13: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) -13: -13: [----------] 37 tests from ReferenceDataTest -13: [ RUN ] ReferenceDataTest.HandlesSimpleData -13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData -13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks -13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesStringBlockData -13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesVectorData -13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesSequenceData -13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData -13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) -13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef -13: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) -13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData -13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) -13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData -13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesIncorrectData -13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType -13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesMissingData -13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUncheckedData -13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence -13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound -13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesAnys -13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree -13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey -13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey -13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue -13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType -13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms) -13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile -13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings -13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace -13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings -13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock -13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices -13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData -13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) -13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds -13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds -13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesReadingValues -13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges -13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges -13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges -13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges -13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) -13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries -13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) -13: [----------] 37 tests from ReferenceDataTest (12 ms total) -13: -13: [----------] 7 tests from FloatingPointDifferenceTest -13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues -13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues -13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign -13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero -13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences -13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero -13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) -13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN -13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) -13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) -13: -13: [----------] 4 tests from FloatingPointToleranceTest -13: [ RUN ] FloatingPointToleranceTest.UlpTolerance -13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) -13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint -13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) -13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp -13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) -13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance -13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) -13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) -13: -13: [----------] 4 tests from XvgTests -13: [ RUN ] XvgTests.CreateFile -13: [ OK ] XvgTests.CreateFile (0 ms) -13: [ RUN ] XvgTests.CheckMissing -13: [ OK ] XvgTests.CheckMissing (0 ms) -13: [ RUN ] XvgTests.CheckExtra -13: [ OK ] XvgTests.CheckExtra (0 ms) -13: [ RUN ] XvgTests.ReadIncorrect -13: [ OK ] XvgTests.ReadIncorrect (0 ms) -13: [----------] 4 tests from XvgTests (1 ms total) -13: -13: [----------] Global test environment tear-down -13: [==========] 75 tests from 7 test suites ran. (18 ms total) -13: [ PASSED ] 75 tests. -13/96 Test #13: TestUtilsUnitTests ........................... Passed 0.21 sec -test 14 - Start 14: TestUtilsMpiUnitTests - -14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" -14: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/testutils/tests -14: Test timeout computed to be: 30 -14: [==========] Running 1 test from 1 test suite. -14: [----------] Global test environment set-up. -14: [----------] 1 test from MpiSelfTest -14: [ RUN ] MpiSelfTest.Runs -14: [ OK ] MpiSelfTest.Runs (0 ms) -14: [----------] 1 test from MpiSelfTest (0 ms total) -14: -14: [----------] Global test environment tear-down -14: [==========] 1 test from 1 test suite ran. (0 ms total) -14: [ PASSED ] 1 test. -14/96 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.27 sec -test 15 - Start 15: UtilityUnitTests - -15: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/UtilityUnitTests.xml" -15: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests -15: Test timeout computed to be: 30 -15: [==========] Running 420 tests from 65 test suites. -15: [----------] Global test environment set-up. -15: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/0.Move -15: [ OK ] AllocatorTest/0.Move (0 ms) -15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/0.Comparison -15: [ OK ] AllocatorTest/0.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/0 (0 ms total) -15: -15: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/1.Move -15: [ OK ] AllocatorTest/1.Move (0 ms) -15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/1.Comparison -15: [ OK ] AllocatorTest/1.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/1 (0 ms total) -15: -15: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator -15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/2.Move -15: [ OK ] AllocatorTest/2.Move (0 ms) -15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/2.Comparison -15: [ OK ] AllocatorTest/2.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/2 (0 ms total) -15: -15: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/3.Move -15: [ OK ] AllocatorTest/3.Move (0 ms) -15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/3.Comparison -15: [ OK ] AllocatorTest/3.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/3 (0 ms total) -15: -15: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/4.Move -15: [ OK ] AllocatorTest/4.Move (0 ms) -15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/4.Comparison -15: [ OK ] AllocatorTest/4.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/4 (0 ms total) -15: -15: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> -15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment -15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment -15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment -15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) -15: [ RUN ] AllocatorTest/5.Move -15: [ OK ] AllocatorTest/5.Move (0 ms) -15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory -15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) -15: [ RUN ] AllocatorTest/5.Comparison -15: [ OK ] AllocatorTest/5.Comparison (0 ms) -15: [----------] 6 tests from AllocatorTest/5 (0 ms total) -15: -15: [----------] 1 test from AllocatorUntypedTest -15: [ RUN ] AllocatorUntypedTest.Comparison -15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) -15: [----------] 1 test from AllocatorUntypedTest (0 ms total) -15: -15: [----------] 4 tests from EmptyArrayRefTest -15: [ RUN ] EmptyArrayRefTest.IsEmpty -15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty -15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) -15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr -15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) -15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull -15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) -15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) -15: -15: [----------] 1 test from EmptyConstArrayRefTest -15: [ RUN ] EmptyConstArrayRefTest.IsEmpty -15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) -15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/8 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) -15: -15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef -15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks -15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks -15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks -15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks -15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks -15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks -15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks -15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) -15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks -15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) -15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) -15: -15: [----------] 8 tests from BoolType -15: [ RUN ] BoolType.ImplicitConversion -15: [ OK ] BoolType.ImplicitConversion (0 ms) -15: [ RUN ] BoolType.FalseByDefault -15: [ OK ] BoolType.FalseByDefault (0 ms) -15: [ RUN ] BoolType.Assignment -15: [ OK ] BoolType.Assignment (0 ms) -15: [ RUN ] BoolType.Copy -15: [ OK ] BoolType.Copy (0 ms) -15: [ RUN ] BoolType.ArrayRefCanBeCreated -15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) -15: [ RUN ] BoolType.CanBeCastToBool -15: [ OK ] BoolType.CanBeCastToBool (0 ms) -15: [ RUN ] BoolType.HasSizeOfBool -15: [ OK ] BoolType.HasSizeOfBool (0 ms) -15: [ RUN ] BoolType.HasAlignmentOfBool -15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) -15: [----------] 8 tests from BoolType (0 ms total) -15: -15: [----------] 4 tests from ArrayRefFromBoolTypeVector -15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty -15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) -15: [ RUN ] ArrayRefFromBoolTypeVector.Works -15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) -15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty -15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) -15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks -15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) -15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) -15: -15: [----------] 7 tests from CStringUtilityTest -15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison -15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) -15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength -15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) -15: [ RUN ] CStringUtilityTest.strip_comment -15: [ OK ] CStringUtilityTest.strip_comment (0 ms) -15: [ RUN ] CStringUtilityTest.upstring -15: [ OK ] CStringUtilityTest.upstring (0 ms) -15: [ RUN ] CStringUtilityTest.ltrim -15: [ OK ] CStringUtilityTest.ltrim (0 ms) -15: [ RUN ] CStringUtilityTest.rtrim -15: [ OK ] CStringUtilityTest.rtrim (0 ms) -15: [ RUN ] CStringUtilityTest.trim -15: [ OK ] CStringUtilityTest.trim (0 ms) -15: [----------] 7 tests from CStringUtilityTest (0 ms total) -15: -15: [----------] 2 tests from DefaultInitializationAllocator -15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization -15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) -15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization -15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) -15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) -15: -15: [----------] 4 tests from EnumerationHelpersTest -15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks -15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) -15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks -15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) -15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe -15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) -15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks -15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) -15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) -15: -15: [----------] 1 test from EnumClassSuitsEnumerationArray -15: [ RUN ] EnumClassSuitsEnumerationArray.Works -15: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) -15: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) -15: -15: [----------] 18 tests from FixedCapacityVectorTest -15: [ RUN ] FixedCapacityVectorTest.IsEmpty -15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ConstructorWorks -15: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.PushWorks -15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.PopWorks -15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ResizeWorks -15: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ClearWorks -15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks -15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.AtThrows -15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) -15: [ RUN ] FixedCapacityVectorTest.IteratorWorks -15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks -15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks -15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks -15: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks -15: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks -15: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks -15: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks -15: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.DataWorks -15: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) -15: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork -15: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) -15: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) -15: -15: [----------] 5 tests from InMemorySerializerTest -15: [ RUN ] InMemorySerializerTest.Roundtrip -15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) -15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap -15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) -15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap -15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) -15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap -15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) -15: [ RUN ] InMemorySerializerTest.SizeIsCorrect -15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) -15: [----------] 5 tests from InMemorySerializerTest (0 ms total) -15: -15: [----------] 4 tests from KeyValueTreeSerializerTest -15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree -15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) -15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject -15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) -15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays -15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) -15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects -15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) -15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) -15: -15: [----------] 7 tests from TreeValueTransformTest -15: [ RUN ] TreeValueTransformTest.SimpleTransforms -15: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) -15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive -15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) -15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject -15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) -15: [ RUN ] TreeValueTransformTest.ObjectFromString -15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) -15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings -15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) -15: [ RUN ] TreeValueTransformTest.ScopedTransformRules -15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) -15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue -15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) -15: [----------] 7 tests from TreeValueTransformTest (0 ms total) -15: -15: [----------] 1 test from TreeValueTransformErrorTest -15: [ RUN ] TreeValueTransformErrorTest.ConversionError -15: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) -15: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) -15: -15: [----------] 9 tests from ListOfLists -15: [ RUN ] ListOfLists.EmptyListOfListsWorks -15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) -15: [ RUN ] ListOfLists.AppendWorks -15: [ OK ] ListOfLists.AppendWorks (0 ms) -15: [ RUN ] ListOfLists.EmptyListWorks -15: [ OK ] ListOfLists.EmptyListWorks (0 ms) -15: [ RUN ] ListOfLists.AppendAccessWorks -15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) -15: [ RUN ] ListOfLists.ClearWorks -15: [ OK ] ListOfLists.ClearWorks (0 ms) -15: [ RUN ] ListOfLists.OutOfRangeAccessThrows -15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) -15: [ RUN ] ListOfLists.FrontAndBackWork -15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) -15: [ RUN ] ListOfLists.ExtractsAndRestores -15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) -15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset -15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) -15: [----------] 9 tests from ListOfLists (0 ms total) -15: -15: [----------] 7 tests from LoggerTest -15: [ RUN ] LoggerTest.EmptyLoggerWorks -15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) -15: [ RUN ] LoggerTest.LogsToStream -15: [ OK ] LoggerTest.LogsToStream (0 ms) -15: [ RUN ] LoggerTest.LogsToFile -15: [ OK ] LoggerTest.LogsToFile (66 ms) -15: [ RUN ] LoggerTest.LevelFilteringWorks -15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) -15: [ RUN ] LoggerTest.LogsToMultipleStreams -15: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) -15: [ RUN ] LoggerTest.LogsToMultipleFiles -15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) -15: [ RUN ] LoggerTest.LogsToStreamAndFile -15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) -15: [----------] 7 tests from LoggerTest (67 ms total) -15: -15: [----------] 7 tests from MessageStringCollectorTest -15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext -15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext -15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages -15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally -15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally -15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct -15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) -15: [ RUN ] MessageStringCollectorTest.CanMoveAssign -15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) -15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) -15: -15: [----------] 1 test from PathTest -15: [ RUN ] PathTest.StripSourcePrefixWorks -15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) -15: [----------] 1 test from PathTest (0 ms total) -15: -15: [----------] 2 tests from PhysicalNodeCommunicatorTest -15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -15: -15: [----------] 5 tests from Range -15: [ RUN ] Range.EmptyRangeWorks -15: [ OK ] Range.EmptyRangeWorks (0 ms) -15: [ RUN ] Range.NonEmptyRangeWorks -15: [ OK ] Range.NonEmptyRangeWorks (0 ms) -15: [ RUN ] Range.BeginEnd -15: [ OK ] Range.BeginEnd (0 ms) -15: [ RUN ] Range.IsInRangeWorks -15: [ OK ] Range.IsInRangeWorks (0 ms) -15: [ RUN ] Range.IteratorWorks -15: [ OK ] Range.IteratorWorks (0 ms) -15: [----------] 5 tests from Range (0 ms total) -15: -15: [----------] 3 tests from ScopeGuardTest -15: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit -15: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) -15: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers -15: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) -15: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions -15: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) -15: [----------] 3 tests from ScopeGuardTest (0 ms total) -15: -15: [----------] 7 tests from StringConvert -15: [ RUN ] StringConvert.NoResultFromEptyString -15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) -15: [ RUN ] StringConvert.ThreeFloatsSuccessfully -15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) -15: [ RUN ] StringConvert.OneIntSucessfully -15: [ OK ] StringConvert.OneIntSucessfully (0 ms) -15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows -15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) -15: [ RUN ] StringConvert.ThrowsWhenWrongSize -15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) -15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows -15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) -15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay -15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) -15: [----------] 7 tests from StringConvert (0 ms total) -15: -15: [----------] 7 tests from StringToEnumValueConverterTest -15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping -15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping -15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping -15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping -15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping -15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping -15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) -15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks -15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) -15: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) -15: -15: [----------] 9 tests from StringUtilityTest -15: [ RUN ] StringUtilityTest.StartsWith -15: [ OK ] StringUtilityTest.StartsWith (0 ms) -15: [ RUN ] StringUtilityTest.EndsWith -15: [ OK ] StringUtilityTest.EndsWith (0 ms) -15: [ RUN ] StringUtilityTest.StripSuffixIfPresent -15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) -15: [ RUN ] StringUtilityTest.StripString -15: [ OK ] StringUtilityTest.StripString (0 ms) -15: [ RUN ] StringUtilityTest.SplitString -15: [ OK ] StringUtilityTest.SplitString (0 ms) -15: [ RUN ] StringUtilityTest.SplitDelimitedString -15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) -15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString -15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) -15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive -15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) -15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength -15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) -15: [----------] 9 tests from StringUtilityTest (0 ms total) -15: -15: [----------] 2 tests from FormatStringTest -15: [ RUN ] FormatStringTest.HandlesBasicFormatting -15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) -15: [ RUN ] FormatStringTest.HandlesLongStrings -15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) -15: [----------] 2 tests from FormatStringTest (0 ms total) -15: -15: [----------] 1 test from StringFormatterTest -15: [ RUN ] StringFormatterTest.HandlesBasicFormatting -15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) -15: [----------] 1 test from StringFormatterTest (0 ms total) -15: -15: [----------] 1 test from formatAndJoinTest -15: [ RUN ] formatAndJoinTest.Works -15: [ OK ] formatAndJoinTest.Works (0 ms) -15: [----------] 1 test from formatAndJoinTest (0 ms total) -15: -15: [----------] 1 test from JoinStringsTest -15: [ RUN ] JoinStringsTest.Works -15: [ OK ] JoinStringsTest.Works (0 ms) -15: [----------] 1 test from JoinStringsTest (0 ms total) -15: -15: [----------] 6 tests from ReplaceAllTest -15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings -15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) -15: [ RUN ] ReplaceAllTest.HandlesNoMatches -15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) -15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds -15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) -15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches -15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) -15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries -15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) -15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches -15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) -15: [----------] 6 tests from ReplaceAllTest (0 ms total) -15: -15: [----------] 10 tests from TextLineWrapperTest -15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings -15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace -15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines -15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) -15: [ RUN ] TextLineWrapperTest.WrapsCorrectly -15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) -15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks -15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesIndent -15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines -15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent -15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) -15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter -15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) -15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace -15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) -15: [----------] 10 tests from TextLineWrapperTest (0 ms total) -15: -15: [----------] 1 test from CompileTimeStringJoin -15: [ RUN ] CompileTimeStringJoin.Works -15: [ OK ] CompileTimeStringJoin.Works (0 ms) -15: [----------] 1 test from CompileTimeStringJoin (0 ms total) -15: -15: [----------] 3 tests from TemplateMPTest -15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum -15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) -15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool -15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) -15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool -15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) -15: [----------] 3 tests from TemplateMPTest (0 ms total) -15: -15: [----------] 6 tests from TextWriterTest -15: [ RUN ] TextWriterTest.WritesLines -15: [ OK ] TextWriterTest.WritesLines (0 ms) -15: [ RUN ] TextWriterTest.WritesLinesInParts -15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) -15: [ RUN ] TextWriterTest.WritesWrappedLines -15: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) -15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper -15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) -15: [ RUN ] TextWriterTest.TracksNewlines -15: [ OK ] TextWriterTest.TracksNewlines (0 ms) -15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace -15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) -15: [----------] 6 tests from TextWriterTest (0 ms total) -15: -15: [----------] 1 test from TypeTraitsTest -15: [ RUN ] TypeTraitsTest.IsIntegralConstant -15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) -15: [----------] 1 test from TypeTraitsTest (0 ms total) -15: -15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) -15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 -15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) -15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) -15: -15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) -15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 -15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) -15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) -15: -15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) -15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 -15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) -15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) -15: -15: [----------] 11 tests from WithInputPaths/PathSearchTest -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) -15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 -15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) -15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) -15: -15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) -15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 -15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) -15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) -15: -15: [----------] Global test environment tear-down -15: [==========] 420 tests from 65 test suites ran. (75 ms total) -15: [ PASSED ] 420 tests. -15: -15: YOU HAVE 1 DISABLED TEST -15: -15/96 Test #15: UtilityUnitTests ............................. Passed 0.29 sec -test 16 - Start 16: UtilityMpiUnitTests - -16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" -16: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/utility/tests -16: Test timeout computed to be: 30 -16: [==========] Running 2 tests from 1 test suite. -16: [----------] Global test environment set-up. -16: [----------] 2 tests from PhysicalNodeCommunicatorTest -16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct -16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) -16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier -16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) -16: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) -16: -16: [----------] Global test environment tear-down -16: [==========] 2 tests from 1 test suite ran. (0 ms total) -16: [ PASSED ] 2 tests. -16/96 Test #16: UtilityMpiUnitTests .......................... Passed 0.27 sec -test 17 - Start 17: GmxlibTests - -17: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxlibTests.xml" -17: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxlib/nonbonded/tests -17: Test timeout computed to be: 30 -17: [==========] Running 78 tests from 2 test suites. -17: [----------] Global test environment set-up. -17: [----------] 72 tests from NBInteraction/NonbondedFepTest -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) -17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 -17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) -17: [----------] 72 tests from NBInteraction/NonbondedFepTest (10 ms total) -17: -17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) -17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 -17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) -17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) -17: -17: [----------] Global test environment tear-down -17: [==========] 78 tests from 2 test suites ran. (11 ms total) -17: [ PASSED ] 78 tests. -17/96 Test #17: GmxlibTests .................................. Passed 0.21 sec -test 18 - Start 18: MdlibUnitTest - -18: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdlibUnitTest.xml" -18: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests -18: Test timeout computed to be: 30 -18: [==========] Running 1032 tests from 27 test suites. -18: [----------] Global test environment set-up. -18: [----------] 3 tests from EffectiveAtomDensity -18: [ RUN ] EffectiveAtomDensity.VolumeIndependence -18: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) -18: [ RUN ] EffectiveAtomDensity.WeightingWorks -18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) -18: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell -18: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) -18: [----------] 3 tests from EffectiveAtomDensity (0 ms total) -18: -18: [----------] 2 tests from AtomNonbondedAndKineticProperties -18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate -18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) -18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork -18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) -18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) -18: -18: [----------] 1 test from VerletBufferConstraintTest -18: [ RUN ] VerletBufferConstraintTest.EqualMasses -18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) -18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) -18: -18: [----------] 1 test from VerletBufferSize -18: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent -18: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) -18: [----------] 1 test from VerletBufferSize (0 ms total) -18: -18: [----------] 6 tests from CalcvirTest -18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox -18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) -18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew -18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) -18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX -18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) -18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY -18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) -18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ -18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) -18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ -18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) -18: [----------] 6 tests from CalcvirTest (0 ms total) -18: -18: [----------] 2 tests from PrEbinTest -18: [ RUN ] PrEbinTest.HandlesAverages -18: [ OK ] PrEbinTest.HandlesAverages (0 ms) -18: [ RUN ] PrEbinTest.HandlesEmptyAverages -18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) -18: [----------] 2 tests from PrEbinTest (0 ms total) -18: -18: [----------] 3 tests from EnergyDriftTracker -18: [ RUN ] EnergyDriftTracker.emptyWorks -18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) -18: [ RUN ] EnergyDriftTracker.onePointWorks -18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) -18: [ RUN ] EnergyDriftTracker.manyPointsWorks -18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) -18: [----------] 3 tests from EnergyDriftTracker (0 ms total) -18: -18: [----------] 4 tests from ShakeTest -18: [ RUN ] ShakeTest.ConstrainsOneBond -18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) -18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds -18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) -18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom -18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) -18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms -18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) -18: [----------] 4 tests from ShakeTest (0 ms total) -18: -18: [----------] 1 test from NullSignalTest -18: [ RUN ] NullSignalTest.NullSignallerWorks -18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) -18: [----------] 1 test from NullSignalTest (0 ms total) -18: -18: [----------] 7 tests from SignalTest -18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace -18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) -18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace -18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) -18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace -18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) -18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace -18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) -18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace -18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) -18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace -18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) -18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace -18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) -18: [----------] 7 tests from SignalTest (0 ms total) -18: -18: [----------] 13 tests from UpdateGroupsTest -18: [ RUN ] UpdateGroupsTest.WithEthaneUA -18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) -18: [ RUN ] UpdateGroupsTest.WithMethane -18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) -18: [ RUN ] UpdateGroupsTest.WithEthane -18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) -18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane -18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) -18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups -18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) -18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite -18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) -18: [ RUN ] UpdateGroupsTest.WithWaterFourSite -18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) -18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle -18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) -18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle -18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) -18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle -18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) -18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes -18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) -18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid -18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) -18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful -18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) -18: [----------] 13 tests from UpdateGroupsTest (0 ms total) -18: -18: [----------] 1 test from UpdateGroupsCog -18: [ RUN ] UpdateGroupsCog.ComputesCogs -18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) -18: [----------] 1 test from UpdateGroupsCog (0 ms total) -18: -18: [----------] 2 tests from WholeMoleculeTransform -18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole -18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) -18: [ RUN ] WholeMoleculeTransform.HandlesReordering -18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) -18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) -18: -18: [----------] 28 tests from WithParameters/ConstraintsTest -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) -18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 -18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (4 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) -18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 -18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) -18: [----------] 28 tests from WithParameters/ConstraintsTest (15 ms total) -18: -18: [----------] 11 tests from WithParameters/EnergyOutputTest -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (1 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (2 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 -18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file -18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (3 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (2 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) -18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 -18: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file -18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) -18: [----------] 11 tests from WithParameters/EnergyOutputTest (21 ms total) -18: -18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) -18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 -18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) -18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) -18: -18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) -18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 -18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) -18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) -18: -18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) -18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 -18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) -18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) -18: -18: [----------] 17 tests from WithParameters/LangevinTest -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) -18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 -18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) -18: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) -18: -18: [----------] 16 tests from WithParameters/LeapFrogTest -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) -18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 -18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) -18: [----------] 16 tests from WithParameters/LeapFrogTest (11 ms total) -18: -18: [----------] 140 tests from Cubic/ParrRahmTest -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) -18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 -18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from Cubic/ParrRahmTest (6 ms total) -18: -18: [----------] 140 tests from Rectilinear/ParrRahmTest -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) -18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 -18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from Rectilinear/ParrRahmTest (6 ms total) -18: -18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 -18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (6 ms total) -18: -18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) -18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 -18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (6 ms total) -18: -18: [----------] 140 tests from TruncOct/ParrRahmTest -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) -18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 -18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from TruncOct/ParrRahmTest (6 ms total) -18: -18: [----------] 140 tests from Other/ParrRahmTest -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) -18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 -18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) -18: [----------] 140 tests from Other/ParrRahmTest (6 ms total) -18: -18: [----------] 13 tests from WithParameters/SettleTest -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) -18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 -18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) -18: [----------] 13 tests from WithParameters/SettleTest (4 ms total) -18: -18: [----------] Global test environment tear-down -18: [==========] 1032 tests from 27 test suites ran. (97 ms total) -18: [ PASSED ] 1032 tests. -18/96 Test #18: MdlibUnitTest ................................ Passed 0.35 sec -test 19 - Start 19: AwhTest - -19: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/AwhTest.xml" -19: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/awh/tests -19: Test timeout computed to be: 30 -19: [==========] Running 25 tests from 9 test suites. -19: [----------] Global test environment set-up. -19: [----------] 3 tests from SerializationTest -19: [ RUN ] SerializationTest.CanSerializeDimParams -19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) -19: [ RUN ] SerializationTest.CanSerializeBiasParams -19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) -19: [ RUN ] SerializationTest.CanSerializeAwhParams -19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) -19: [----------] 3 tests from SerializationTest (0 ms total) -19: -19: [----------] 1 test from BiasTest -19: [ RUN ] BiasTest.DetectsCovering -19: [ OK ] BiasTest.DetectsCovering (0 ms) -19: [----------] 1 test from BiasTest (0 ms total) -19: -19: [----------] 1 test from biasGridTest -19: [ RUN ] biasGridTest.neighborhood -19: [ OK ] biasGridTest.neighborhood (0 ms) -19: [----------] 1 test from biasGridTest (0 ms total) -19: -19: [----------] 2 tests from BiasFepLambdaStateTest -19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering -19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) -19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy -19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) -19: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) -19: -19: [----------] 8 tests from WithParameters/BiasTest -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) -19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 -19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) -19: [----------] 8 tests from WithParameters/BiasTest (3 ms total) -19: -19: [----------] 2 tests from WithParameters/BiasStateTest -19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 -19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) -19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 -19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) -19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) -19: -19: [----------] 1 test from WithParameters/UserInputTest -19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 -19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) -19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) -19: -19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest -19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 -19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (4 ms) -19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 -19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) -19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 -19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) -19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 -19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) -19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (16 ms total) -19: -19: [----------] 3 tests from WithParameters/FrictionMetricTest -19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 -19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) -19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 -19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) -19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 -19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (10 ms) -19: [----------] 3 tests from WithParameters/FrictionMetricTest (12 ms total) -19: -19: [----------] Global test environment tear-down -19: [==========] 25 tests from 9 test suites ran. (38 ms total) -19: [ PASSED ] 25 tests. -19/96 Test #19: AwhTest ...................................... Passed 0.23 sec -test 20 - Start 20: DensityFittingAppliedForcesUnitTest - -20: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" -20: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/densityfitting/tests -20: Test timeout computed to be: 30 -20: [==========] Running 18 tests from 4 test suites. -20: [----------] Global test environment set-up. -20: [----------] 2 tests from DensityFittingTest -20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows -20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) -20: [ RUN ] DensityFittingTest.SingleAtom -20: [ OK ] DensityFittingTest.SingleAtom (0 ms) -20: [----------] 2 tests from DensityFittingTest (0 ms total) -20: -20: [----------] 7 tests from DensityFittingAmplitudeLookupTest -20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity -20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge -20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses -20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign -20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct -20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign -20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) -20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct -20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) -20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) -20: -20: [----------] 1 test from DensityFittingForceProviderState -20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving -20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) -20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) -20: -20: [----------] 8 tests from DensityFittingOptionsTest -20: [ RUN ] DensityFittingOptionsTest.DefaultParameters -20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) -20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive -20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) -20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive -20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive -20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) -20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup -20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt -20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) -20: [ RUN ] DensityFittingOptionsTest.KvtToInternal -20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) -20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent -20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) -20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) -20: -20: [----------] Global test environment tear-down -20: [==========] 18 tests from 4 test suites ran. (1 ms total) -20: [ PASSED ] 18 tests. -20/96 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.19 sec -test 21 - Start 21: QMMMAppliedForcesUnitTest - -21: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" -21: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests -21: Test timeout computed to be: 30 -21: [==========] Running 21 tests from 5 test suites. -21: [----------] Global test environment set-up. -21: [----------] 3 tests from QMMMInputGeneratorTest -21: [ RUN ] QMMMInputGeneratorTest.CanConstruct -21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) -21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink -21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) -21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink -21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) -21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) -21: -21: [----------] 7 tests from QMMMTopologyPreprocessorTest -21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct -21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 21.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to 1824473084 -21: -21: Generated 10 of the 10 non-bonded parameter combinations -21: -21: Generated 10 of the 10 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Water residues -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (4 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 21.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to -74897 -21: -21: Generated 10 of the 10 non-bonded parameter combinations -21: -21: Generated 10 of the 10 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Water residues -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (4 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 21.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to -76054689 -21: -21: Generated 10 of the 10 non-bonded parameter combinations -21: -21: Generated 10 of the 10 1-4 parameter combinations -21: -21: Excluding 2 bonded neighbours molecule type 'SOL' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -21: Analysing residue names: -21: There are: 4 Water residues -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (3 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: Number of degrees of freedom in T-Coupling group rest is 63.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -21: NVE simulation: will use the initial temperature of 129.093 K for -21: determining the Verlet buffer size -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to -149946576 -21: -21: Generated 2145 of the 2145 non-bonded parameter combinations -21: -21: Generated 2145 of the 2145 1-4 parameter combinations -21: -21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -21: Analysing residue names: -21: There are: 3 Protein residues -21: Analysing Protein... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (8 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Generating 1-4 interactions: fudge = 0.5 -21: -21: NOTE 2 [file unknown]: -21: You are using constraints on all bonds, whereas the forcefield has been -21: parametrized only with constraints involving hydrogen atoms. We suggest -21: using constraints = h-bonds instead, this will also improve performance. -21: -21: -21: NOTE 3 [file unknown]: -21: For energy conservation with LINCS, lincs_iter should be 2 or larger. -21: -21: -21: Number of degrees of freedom in T-Coupling group rest is 42.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -21: NVE simulation: will use the initial temperature of 193.640 K for -21: determining the Verlet buffer size -21: -21: -21: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 5 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to -230687234 -21: -21: Generated 2145 of the 2145 non-bonded parameter combinations -21: -21: Generated 2145 of the 2145 1-4 parameter combinations -21: -21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -21: -21: turning all bonds into constraints... -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -21: Analysing residue names: -21: There are: 3 Protein residues -21: Analysing Protein... -21: -21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -21: -21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -21: -21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -21: -21: Note that mdrun will redetermine rlist based on the actual pair-list setup -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (9 ms) -21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites -21: -21: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -21: For a correct single-point energy evaluation with nsteps = 0, use -21: continuation = yes to avoid constraining the input coordinates. -21: -21: Number of degrees of freedom in T-Coupling group rest is 45.00 -21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -21: -21: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -21: NVE simulation with an initial temperature of zero: will use a Verlet -21: buffer of 10%. Check your energy drift! -21: -21: -21: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: -21: You are using a plain Coulomb cut-off, which might produce artifacts. -21: You might want to consider using PME electrostatics. -21: -21: -21: -21: There were 3 NOTEs -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -21: Setting the LD random seed to -135463042 -21: -21: Generated 3 of the 6 non-bonded parameter combinations -21: -21: Excluding 3 bonded neighbours molecule type 'VSTEST' -21: -21: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -21: -21: Cleaning up constraints and constant bonded interactions with virtual sites -21: Analysing residue names: -21: There are: 1 Other residues -21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -21: -21: This run will generate roughly 0 Mb of data -21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) -21: [----------] 7 tests from QMMMTopologyPreprocessorTest (35 ms total) -21: -21: [----------] 9 tests from QMMMOptionsTest -21: [ RUN ] QMMMOptionsTest.DefaultParameters -21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) -21: [ RUN ] QMMMOptionsTest.OptionSetsActive -21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) -21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive -21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive -21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) -21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup -21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) -21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup -21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) -21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup -21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) -21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack -21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) -21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing -21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) -21: [----------] 9 tests from QMMMOptionsTest (1 ms total) -21: -21: [----------] 1 test from QMMMForceProviderTest -21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot -21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) -21: [----------] 1 test from QMMMForceProviderTest (0 ms total) -21: -21: [----------] 1 test from QMMMTest -21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows -21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) -21: [----------] 1 test from QMMMTest (0 ms total) -21: -21: [----------] Global test environment tear-down -21: [==========] 21 tests from 5 test suites ran. (37 ms total) -21: [ PASSED ] 21 tests. -21/96 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.23 sec -test 22 - Start 22: ColvarsAppliedForcesUnitTest - -22: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" -22: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests -22: Test timeout computed to be: 30 -22: [==========] Running 16 tests from 4 test suites. -22: [----------] Global test environment set-up. -22: [----------] 1 test from ColvarsTest -22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows -22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) -22: [----------] 1 test from ColvarsTest (0 ms total) -22: -22: [----------] 6 tests from ColvarsOptionsTest -22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive -22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive -22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) -22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive -22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) -22: [ RUN ] ColvarsOptionsTest.OptionSetsActive -22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) -22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -312541714 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (5 ms) -22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename -22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) -22: [----------] 6 tests from ColvarsOptionsTest (5 ms total) -22: -22: [----------] 4 tests from ColvarsPreProcessorTest -22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -873596937 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (3 ms) -22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to 2147483135 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) -22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -1082689877 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (4 ms) -22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -847290370 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (4 ms) -22: [----------] 4 tests from ColvarsPreProcessorTest (17 ms total) -22: -22: [----------] 5 tests from ColvarsForceProviderTest -22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot -22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) -22: [ RUN ] ColvarsForceProviderTest.SimpleInputs -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -34607593 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsForceProviderTest.SimpleInputs (4 ms) -22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to -52452185 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (12 ms) -22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 21.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -22: NVE simulation with an initial temperature of zero: will use a Verlet -22: buffer of 10%. Check your energy drift! -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to 2122251991 -22: -22: Generated 10 of the 10 non-bonded parameter combinations -22: -22: Generated 10 of the 10 1-4 parameter combinations -22: -22: Excluding 2 bonded neighbours molecule type 'SOL' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -22: Analysing residue names: -22: There are: 4 Water residues -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (14 ms) -22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine -22: -22: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -22: For a correct single-point energy evaluation with nsteps = 0, use -22: continuation = yes to avoid constraining the input coordinates. -22: -22: Generating 1-4 interactions: fudge = 0.5 -22: Number of degrees of freedom in T-Coupling group rest is 66.00 -22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -22: -22: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -22: NVE simulation: will use the initial temperature of 300.368 K for -22: determining the Verlet buffer size -22: -22: -22: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: -22: You are using a plain Coulomb cut-off, which might produce artifacts. -22: You might want to consider using PME electrostatics. -22: -22: -22: -22: There were 3 NOTEs -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -22: Setting the LD random seed to 2130696110 -22: -22: Generated 2211 of the 2211 non-bonded parameter combinations -22: -22: Generated 2211 of the 2211 1-4 parameter combinations -22: -22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -22: -22: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -22: Analysing residue names: -22: There are: 2 Protein residues -22: Analysing Protein... -22: -22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -22: -22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -22: -22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -22: -22: Note that mdrun will redetermine rlist based on the actual pair-list setup -22: -22: This run will generate roughly 0 Mb of data -22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (20 ms) -22: [----------] 5 tests from ColvarsForceProviderTest (53 ms total) -22: -22: [----------] Global test environment tear-down -22: [==========] 16 tests from 4 test suites ran. (76 ms total) -22: [ PASSED ] 16 tests. -22/96 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.28 sec -test 23 - Start 23: PlumedAppliedForcesUnitTests - -23: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" -23: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests -23: Test timeout computed to be: 30 -23: [==========] Running 8 tests from 1 test suite. -23: [----------] Global test environment set-up. -23: [----------] 8 tests from PlumedOptionsTest -23: [ RUN ] PlumedOptionsTest.defaultConstructor -23: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) -23: [ RUN ] PlumedOptionsTest.setTimeStep -23: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) -23: [ RUN ] PlumedOptionsTest.setStartingBehavior -23: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) -23: [ RUN ] PlumedOptionsTest.setPlumedFile -23: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) -23: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet -23: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) -23: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data -23: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) -23: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant -23: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) -23: [ RUN ] PlumedOptionsTest.setTopology -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 21.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: -23: NOTE 2 [file angles1.top, line 72]: -23: In moleculetype 'butane' 4 atoms are not bound by a potential or -23: constraint to any other atom in the same moleculetype. Although -23: technically this might not cause issues in a simulation, this often means -23: that the user forgot to add a bond/potential/constraint or put multiple -23: molecules in the same moleculetype definition by mistake. Run with -v to -23: get information for each atom. -23: -23: Number of degrees of freedom in T-Coupling group rest is 9.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: -23: NVE simulation: will use the initial temperature of 238.919 K for -23: determining the Verlet buffer size -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Number of degrees of freedom in T-Coupling group rest is 17493.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: -23: NVE simulation: will use the initial temperature of 67.983 K for -23: determining the Verlet buffer size -23: -23: -23: There were 2 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Number of degrees of freedom in T-Coupling group rest is 9.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: There were 2 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Number of degrees of freedom in T-Coupling group rest is 9.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -23: NVE simulation with an initial temperature of zero: will use a Verlet -23: buffer of 10%. Check your energy drift! -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: -23: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -23: For a correct single-point energy evaluation with nsteps = 0, use -23: continuation = yes to avoid constraining the input coordinates. -23: -23: Generating 1-4 interactions: fudge = 0.5 -23: Number of degrees of freedom in T-Coupling group rest is 18.00 -23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -23: -23: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -23: NVE simulation: will use the initial temperature of 135.187 K for -23: determining the Verlet buffer size -23: -23: -23: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: -23: You are using a plain Coulomb cut-off, which might produce artifacts. -23: You might want to consider using PME electrostatics. -23: -23: -23: -23: There were 3 NOTEs -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -23: Setting the LD random seed to -21629482 -23: -23: Generated 10 of the 10 non-bonded parameter combinations -23: -23: Generated 10 of the 10 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Water residues -23: -23: This run will generate roughly 0 Mb of data -23: Setting the LD random seed to -44042629 -23: -23: Generated 3 of the 3 non-bonded parameter combinations -23: -23: Excluding 3 bonded neighbours molecule type 'butane' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/angles1.gro' -23: Analysing residue names: -23: There are: 1 Other residues -23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: Setting the LD random seed to -336077827 -23: -23: Generated 1 of the 1 non-bonded parameter combinations -23: -23: Excluding 1 bonded neighbours molecule type 'Argon' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon5832.gro' -23: Analysing residue names: -23: There are: 5832 Other residues -23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: Setting the LD random seed to 2113759198 -23: -23: Generated 1 of the 1 non-bonded parameter combinations -23: -23: Excluding 1 bonded neighbours molecule type 'ArgonA' -23: -23: Excluding 1 bonded neighbours molecule type 'ArgonB' -23: -23: Excluding 1 bonded neighbours molecule type 'ArgonC' -23: -23: Excluding 1 bonded neighbours molecule type 'ArgonD' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -23: Analysing residue names: -23: There are: 4 Other residues -23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -23: -23: This run will generate roughly 0 Mb of data -23: Setting the LD random seed to -612370697 -23: -23: Generated 1 of the 1 non-bonded parameter combinations -23: -23: Excluding 1 bonded neighbours molecule type 'Dipole' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -23: Analysing residue names: -23: There are: 2 Other residues -23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -23: -23: This run will generate roughly 0 Mb of data -23: Setting the LD random seed to 1795021565 -23: -23: Generated 331705 of the 331705 non-bonded parameter combinations -23: -23: Generated 331705 of the 331705 1-4 parameter combinations -23: -23: Excluding 2 bonded neighbours molecule type 'SOL' -23: -23: Excluding 3 bonded neighbours molecule type 'methane' -23: -23: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc_and_methane.gro' -23: Analysing residue names: -23: There are: 1 Water residues -23: There are: 1 Other residues -23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -23: -23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K -23: -23: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -23: -23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -23: -23: Note that mdrun will redetermine rlist based on the actual pair-list setup -23: -23: This run will generate roughly 0 Mb of data -23: [ OK ] PlumedOptionsTest.setTopology (278 ms) -23: [----------] 8 tests from PlumedOptionsTest (279 ms total) -23: -23: [----------] Global test environment tear-down -23: [==========] 8 tests from 1 test suite ran. (279 ms total) -23: [ PASSED ] 8 tests. -23/96 Test #23: PlumedAppliedForcesUnitTests ................. Passed 0.47 sec -test 24 - Start 24: PlumedMDTests - -24: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/PlumedMDTests.xml" -24: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/plumed/tests -24: Test timeout computed to be: 600 -24: [==========] Running 2 tests from 1 test suite. -24: [----------] Global test environment set-up. -24: [----------] 2 tests from SimplePlumedMD/PlumedRun -24: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 -24: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -24: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) -24: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -24: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped -24: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. -24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) -24: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) -24: -24: [----------] Global test environment tear-down -24: [==========] 2 tests from 1 test suite ran. (16 ms total) -24: [ PASSED ] 0 tests. -24: [ SKIPPED ] 2 tests, listed below: -24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 -24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 -24/96 Test #24: PlumedMDTests ................................ Passed 0.32 sec -test 25 - Start 25: NNPotAppliedForcesUnitTest - -25: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" -25: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests -25: Test timeout computed to be: 30 -25: [==========] Running 12 tests from 4 test suites. -25: [----------] Global test environment set-up. -25: [----------] 1 test from NNPotTest -25: [ RUN ] NNPotTest.ForceProviderLackingInputThrows -25: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) -25: [----------] 1 test from NNPotTest (0 ms total) -25: -25: [----------] 5 tests from NNPotOptionsTest -25: [ RUN ] NNPotOptionsTest.DefaultParameters -25: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) -25: [ RUN ] NNPotOptionsTest.OptionSetsActive -25: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) -25: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive -25: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) -25: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive -25: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) -25: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack -25: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) -25: [----------] 5 tests from NNPotOptionsTest (0 ms total) -25: -25: [----------] 5 tests from NNPotTopologyPreprocessorTest -25: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct -25: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) -25: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion -25: -25: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -25: For a correct single-point energy evaluation with nsteps = 0, use -25: continuation = yes to avoid constraining the input coordinates. -25: -25: Generating 1-4 interactions: fudge = 0.5 -25: Number of degrees of freedom in T-Coupling group rest is 21.00 -25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -25: -25: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -25: NVE simulation with an initial temperature of zero: will use a Verlet -25: buffer of 10%. Check your energy drift! -25: -25: -25: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: -25: You are using a plain Coulomb cut-off, which might produce artifacts. -25: You might want to consider using PME electrostatics. -25: -25: -25: -25: There were 3 NOTEs -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Setting the LD random seed to -67642371 -25: -25: Generated 10 of the 10 non-bonded parameter combinations -25: -25: Generated 10 of the 10 1-4 parameter combinations -25: -25: Excluding 2 bonded neighbours molecule type 'SOL' -25: -25: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -25: Analysing residue names: -25: There are: 4 Water residues -25: -25: This run will generate roughly 0 Mb of data -25: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) -25: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion -25: -25: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -25: For a correct single-point energy evaluation with nsteps = 0, use -25: continuation = yes to avoid constraining the input coordinates. -25: -25: Generating 1-4 interactions: fudge = 0.5 -25: Number of degrees of freedom in T-Coupling group rest is 21.00 -25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -25: -25: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -25: NVE simulation with an initial temperature of zero: will use a Verlet -25: buffer of 10%. Check your energy drift! -25: -25: -25: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: -25: You are using a plain Coulomb cut-off, which might produce artifacts. -25: You might want to consider using PME electrostatics. -25: -25: -25: -25: There were 3 NOTEs -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Setting the LD random seed to 1819256667 -25: -25: Generated 10 of the 10 non-bonded parameter combinations -25: -25: Generated 10 of the 10 1-4 parameter combinations -25: -25: Excluding 2 bonded neighbours molecule type 'SOL' -25: -25: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -25: Analysing residue names: -25: There are: 4 Water residues -25: -25: This run will generate roughly 0 Mb of data -25: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (3 ms) -25: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints -25: -25: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -25: For a correct single-point energy evaluation with nsteps = 0, use -25: continuation = yes to avoid constraining the input coordinates. -25: -25: Generating 1-4 interactions: fudge = 0.5 -25: Number of degrees of freedom in T-Coupling group rest is 63.00 -25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -25: -25: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -25: NVE simulation: will use the initial temperature of 129.093 K for -25: determining the Verlet buffer size -25: -25: -25: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: -25: You are using a plain Coulomb cut-off, which might produce artifacts. -25: You might want to consider using PME electrostatics. -25: -25: -25: -25: There were 3 NOTEs -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Setting the LD random seed to -270569473 -25: -25: Generated 2145 of the 2145 non-bonded parameter combinations -25: -25: Generated 2145 of the 2145 1-4 parameter combinations -25: -25: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -25: -25: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -25: Analysing residue names: -25: There are: 3 Protein residues -25: Analysing Protein... -25: -25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K -25: -25: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm -25: -25: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm -25: -25: Note that mdrun will redetermine rlist based on the actual pair-list setup -25: -25: This run will generate roughly 0 Mb of data -25: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (187 ms) -25: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints -25: -25: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -25: For a correct single-point energy evaluation with nsteps = 0, use -25: continuation = yes to avoid constraining the input coordinates. -25: -25: Generating 1-4 interactions: fudge = 0.5 -25: -25: NOTE 2 [file unknown]: -25: You are using constraints on all bonds, whereas the forcefield has been -25: parametrized only with constraints involving hydrogen atoms. We suggest -25: using constraints = h-bonds instead, this will also improve performance. -25: -25: -25: NOTE 3 [file unknown]: -25: For energy conservation with LINCS, lincs_iter should be 2 or larger. -25: -25: -25: Number of degrees of freedom in T-Coupling group rest is 42.00 -25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -25: -25: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -25: NVE simulation: will use the initial temperature of 193.640 K for -25: determining the Verlet buffer size -25: -25: -25: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: -25: You are using a plain Coulomb cut-off, which might produce artifacts. -25: You might want to consider using PME electrostatics. -25: -25: -25: -25: There were 5 NOTEs -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -25: Setting the LD random seed to -226891905 -25: -25: Generated 2145 of the 2145 non-bonded parameter combinations -25: -25: Generated 2145 of the 2145 1-4 parameter combinations -25: -25: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -25: -25: turning all bonds into constraints... -25: -25: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -25: Analysing residue names: -25: There are: 3 Protein residues -25: Analysing Protein... -25: -25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K -25: -25: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm -25: -25: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm -25: -25: Note that mdrun will redetermine rlist based on the actual pair-list setup -25: -25: This run will generate roughly 0 Mb of data -25: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (185 ms) -25: [----------] 5 tests from NNPotTopologyPreprocessorTest (380 ms total) -25: -25: [----------] 1 test from NNPotForceProviderTest -25: [ RUN ] NNPotForceProviderTest.CanConstruct -25: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) -25: [----------] 1 test from NNPotForceProviderTest (0 ms total) -25: -25: [----------] Global test environment tear-down -25: [==========] 12 tests from 4 test suites ran. (381 ms total) -25: [ PASSED ] 12 tests. -25/96 Test #25: NNPotAppliedForcesUnitTest ................... Passed 0.66 sec -test 26 - Start 26: AppliedForcesUnitTest - -26: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" -26: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/applied_forces/tests -26: Test timeout computed to be: 30 -26: [==========] Running 3 tests from 1 test suite. -26: [----------] Global test environment set-up. -26: [----------] 3 tests from ElectricFieldTest -26: [ RUN ] ElectricFieldTest.Static -26: [ OK ] ElectricFieldTest.Static (0 ms) -26: [ RUN ] ElectricFieldTest.Oscillating -26: [ OK ] ElectricFieldTest.Oscillating (0 ms) -26: [ RUN ] ElectricFieldTest.Pulsed -26: [ OK ] ElectricFieldTest.Pulsed (0 ms) -26: [----------] 3 tests from ElectricFieldTest (0 ms total) -26: -26: [----------] Global test environment tear-down -26: [==========] 3 tests from 1 test suite ran. (0 ms total) -26: [ PASSED ] 3 tests. -26/96 Test #26: AppliedForcesUnitTest ........................ Passed 0.19 sec -test 27 - Start 27: ListedForcesTest - -27: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/ListedForcesTest.xml" -27: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/listed_forces/tests -27: Test timeout computed to be: 30 -27: [==========] Running 132 tests from 9 test suites. -27: [----------] Global test environment set-up. -27: [----------] 24 tests from Bond/ListedForcesTest -27: [ RUN ] Bond/ListedForcesTest.Ifunc/0 -27: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/1 -27: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/2 -27: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/3 -27: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/4 -27: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/5 -27: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/6 -27: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/7 -27: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/8 -27: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/9 -27: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/10 -27: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/11 -27: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/12 -27: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/13 -27: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/14 -27: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/15 -27: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/16 -27: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/17 -27: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/18 -27: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/19 -27: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/20 -27: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/21 -27: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/22 -27: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) -27: [ RUN ] Bond/ListedForcesTest.Ifunc/23 -27: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) -27: [----------] 24 tests from Bond/ListedForcesTest (4 ms total) -27: -27: [----------] 33 tests from Angle/ListedForcesTest -27: [ RUN ] Angle/ListedForcesTest.Ifunc/0 -27: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/1 -27: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/2 -27: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/3 -27: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/4 -27: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/5 -27: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/6 -27: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/7 -27: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/8 -27: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/9 -27: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/10 -27: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/11 -27: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/12 -27: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/13 -27: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/14 -27: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/15 -27: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/16 -27: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/17 -27: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/18 -27: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/19 -27: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/20 -27: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/21 -27: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/22 -27: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/23 -27: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/24 -27: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/25 -27: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/26 -27: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/27 -27: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/28 -27: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/29 -27: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/30 -27: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/31 -27: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) -27: [ RUN ] Angle/ListedForcesTest.Ifunc/32 -27: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) -27: [----------] 33 tests from Angle/ListedForcesTest (4 ms total) -27: -27: [----------] 18 tests from Dihedral/ListedForcesTest -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) -27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 -27: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) -27: [----------] 18 tests from Dihedral/ListedForcesTest (2 ms total) -27: -27: [----------] 12 tests from Polarize/ListedForcesTest -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) -27: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 -27: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) -27: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) -27: -27: [----------] 18 tests from Restraints/ListedForcesTest -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) -27: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 -27: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) -27: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) -27: -27: [----------] 3 tests from BondZeroLength/ListedForcesTest -27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 -27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 -27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 -27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) -27: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) -27: -27: [----------] 3 tests from AngleZero/ListedForcesTest -27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 -27: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) -27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 -27: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) -27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 -27: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) -27: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) -27: -27: [----------] 12 tests from 14Interaction/ListedForcesPairsTest -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) -27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 -27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) -27: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) -27: -27: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) -27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 -27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) -27: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) -27: -27: [----------] Global test environment tear-down -27: [==========] 132 tests from 9 test suites ran. (17 ms total) -27: [ PASSED ] 132 tests. -27/96 Test #27: ListedForcesTest ............................. Passed 0.22 sec -test 28 - Start 28: NbnxmTests - -28: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbnxmTests.xml" -28: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/nbnxm/tests -28: Test timeout computed to be: 30 -28: [==========] Running 383 tests from 4 test suites. -28: [----------] Global test environment set-up. -28: [----------] 18 tests from KernelSetupTest -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF -28: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut -28: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable -28: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin -28: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald -28: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) -28: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin -28: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom -28: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone -28: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch -28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) -28: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows -28: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) -28: [----------] 18 tests from KernelSetupTest (0 ms total) -28: -28: [----------] 2 tests from SimdEnergyAccumulatorTest -28: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM -28: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) -28: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM -28: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) -28: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) -28: -28: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest -28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 -28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) -28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 -28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) -28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 -28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) -28: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) -28: -28: [----------] 360 tests from Combinations/NbnxmKernelTest -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (4 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (3 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped -28: Analytical Ewald is not implemented for the plain-C kernel, skip this test -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped -28: There are no combination rule versions of the plain-C kernel -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped -28: Cannot test or generate data for 2xNN kernels without suitable SIMD support -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) -28: [----------] 360 tests from Combinations/NbnxmKernelTest (376 ms total) -28: -28: [----------] Global test environment tear-down -28: [==========] 383 tests from 4 test suites ran. (377 ms total) -28: [ PASSED ] 185 tests. -28: [ SKIPPED ] 198 tests, listed below: -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom -28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom -28/96 Test #28: NbnxmTests ................................... Passed 0.58 sec -test 29 - Start 29: NbnxmGpuTests - -29: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/NbnxmGpuTests.xml" -29: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/nbnxm/tests -29: Test timeout computed to be: 30 -29: [==========] Running 0 tests from 0 test suites. -29: [==========] 0 tests from 0 test suites ran. (0 ms total) -29: [ PASSED ] 0 tests. -29/96 Test #29: NbnxmGpuTests ................................ Passed 0.22 sec -test 30 - Start 30: CommandLineUnitTests - -30: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" -30: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests -30: Test timeout computed to be: 30 -30: [==========] Running 60 tests from 7 test suites. -30: [----------] Global test environment set-up. -30: [----------] 3 tests from CommandLineHelpModuleTest -30: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp -30: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) -30: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic -30: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) -30: [ RUN ] CommandLineHelpModuleTest.ExportsHelp -30: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) -30: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) -30: -30: [----------] 7 tests from CommandLineHelpWriterTest -30: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes -30: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables -30: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions -30: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions -30: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups -30: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText -30: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) -30: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues -30: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) -30: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) -30: -30: [----------] 6 tests from CommandLineModuleManagerTest -30: [ RUN ] CommandLineModuleManagerTest.RunsModule -30: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) -30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp -30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) -30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet -30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) -30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH -30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) -30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule -30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) -30: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames -30: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) -30: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) -30: -30: [----------] 13 tests from CommandLineParserTest -30: [ RUN ] CommandLineParserTest.HandlesSingleValues -30: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument -30: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument -30: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) -30: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument -30: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers -30: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesString -30: [ OK ] CommandLineParserTest.HandlesString (0 ms) -30: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues -30: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix -30: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers -30: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) -30: [ RUN ] CommandLineParserTest.HandlesSkipUnknown -30: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) -30: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault -30: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) -30: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments -30: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) -30: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions -30: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) -30: [----------] 13 tests from CommandLineParserTest (0 ms total) -30: -30: [----------] 6 tests from CommandLineProgramContextTest -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath -30: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath -30: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath -30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory -30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink -30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) -30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink -30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) -30: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) -30: -30: [----------] 3 tests from OutputNamesTest -30: [ RUN ] OutputNamesTest.CanBeSuffixed -30: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) -30: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend -30: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) -30: [ RUN ] OutputNamesTest.CanHavePartNumberAdded -30: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) -30: [----------] 3 tests from OutputNamesTest (0 ms total) -30: -30: [----------] 22 tests from ParseCommonArgsTest -30: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs -30: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesInt64Args -30: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesRealArgs -30: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesStringArgs -30: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs -30: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum -30: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs -30: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs -30: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit -30: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs -30: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesFileArgs -30: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults -30: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName -30: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) -30: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension -30: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) -30: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles -30: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) -30: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles -30: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) -30: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified -30: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) -30: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles -30: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) -30: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension -30: Value is /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo -30: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) -30: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile -30: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) -30: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName -30: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms) -30: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs -30: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) -30: [----------] 22 tests from ParseCommonArgsTest (5 ms total) -30: -30: [----------] Global test environment tear-down -30: [==========] 60 tests from 7 test suites ran. (10 ms total) -30: [ PASSED ] 60 tests. -30/96 Test #30: CommandLineUnitTests ......................... Passed 0.20 sec -test 31 - Start 31: DomDecTests - -31: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/DomDecTests.xml" -31: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/domdec/tests -31: Test timeout computed to be: 30 -31: [==========] Running 9 tests from 2 test suites. -31: [----------] Global test environment set-up. -31: [----------] 7 tests from HashedMap -31: [ RUN ] HashedMap.InsertsFinds -31: [ OK ] HashedMap.InsertsFinds (0 ms) -31: [ RUN ] HashedMap.NegativeKeysWork -31: [ OK ] HashedMap.NegativeKeysWork (0 ms) -31: [ RUN ] HashedMap.InsertsErases -31: [ OK ] HashedMap.InsertsErases (0 ms) -31: [ RUN ] HashedMap.InsertsOrAssigns -31: [ OK ] HashedMap.InsertsOrAssigns (0 ms) -31: [ RUN ] HashedMap.Clears -31: [ OK ] HashedMap.Clears (0 ms) -31: [ RUN ] HashedMap.LinkedEntries -31: [ OK ] HashedMap.LinkedEntries (0 ms) -31: [ RUN ] HashedMap.ResizesTable -31: [ OK ] HashedMap.ResizesTable (0 ms) -31: [----------] 7 tests from HashedMap (0 ms total) -31: -31: [----------] 2 tests from LocalAtomSetManager -31: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet -31: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) -31: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices -31: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) -31: [----------] 2 tests from LocalAtomSetManager (0 ms total) -31: -31: [----------] Global test environment tear-down -31: [==========] 9 tests from 2 test suites ran. (0 ms total) -31: [ PASSED ] 9 tests. -31/96 Test #31: DomDecTests .................................. Passed 0.19 sec -test 32 - Start 32: DomDecMpiTests - -32: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/DomDecMpiTests.xml" -32: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/domdec/tests -32: Test timeout computed to be: 30 -32: [==========] Running 4 tests from 1 test suite. -32: [----------] Global test environment set-up. -32: [----------] 4 tests from HaloExchangeTest -32: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse -32: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) -32: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses -32: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) -32: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim -32: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) -32: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 -32: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) -32: [----------] 4 tests from HaloExchangeTest (0 ms total) -32: -32: [----------] Global test environment tear-down -32: [==========] 4 tests from 1 test suite ran. (0 ms total) -32: [ PASSED ] 4 tests. -32/96 Test #32: DomDecMpiTests ............................... Passed 0.34 sec -test 33 - Start 33: EwaldUnitTests - -33: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/EwaldUnitTests.xml" -33: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/ewald/tests -33: Test timeout computed to be: 30 -33: [==========] Running 407 tests from 9 test suites. -33: [----------] Global test environment set-up. -33: [----------] 6 tests from SeparatePmeRanksPermittedTest -33: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons -33: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) -33: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled -33: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) -33: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag -33: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) -33: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText -33: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) -33: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText -33: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) -33: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText -33: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) -33: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) -33: -33: [----------] 108 tests from Pme_SplineAndSpreadTest -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (2 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) -33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread -33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) -33: [----------] 108 tests from Pme_SplineAndSpreadTest (91 ms total) -33: -33: [----------] 64 tests from Pme_SolveTest -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [----------] 64 tests from Pme_SolveTest (13 ms total) -33: -33: [----------] 32 tests from PmeDiffEwaldQ_SolveTest -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (5 ms total) -33: -33: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy -33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) -33: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (7 ms total) -33: -33: [----------] 64 tests from PmeDiffEps_SolveTest -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped -33: Test is being skipped because: -33: CPU PME solve does not implement XYZ grid ordering -33: -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) -33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy -33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) -33: [----------] 64 tests from PmeDiffEps_SolveTest (12 ms total) -33: -33: [----------] 72 tests from Pme_GatherTest -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) -33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms -33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) -33: [----------] 72 tests from Pme_GatherTest (19 ms total) -33: -33: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest -33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 -33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) -33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 -33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) -33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 -33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) -33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 -33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) -33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 -33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) -33: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) -33: -33: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (3 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) -33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 -33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) -33: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (29 ms total) -33: -33: [----------] Global test environment tear-down -33: [==========] 407 tests from 9 test suites ran. (182 ms total) -33: [ PASSED ] 311 tests. -33: [ SKIPPED ] 96 tests, listed below: -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ -33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy -33/96 Test #33: EwaldUnitTests ............................... Passed 0.41 sec -test 34 - Start 34: FFTUnitTests - -34: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/FFTUnitTests.xml" -34: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/fft/tests -34: Test timeout computed to be: 1920 -34: [==========] Running 15 tests from 4 test suites. -34: [----------] Global test environment set-up. -34: [----------] 2 tests from ManyFFTTest -34: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test -34: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (4 ms) -34: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test -34: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (13 ms) -34: [----------] 2 tests from ManyFFTTest (18 ms total) -34: -34: [----------] 1 test from FFTTest -34: [ RUN ] FFTTest.Real2DLength18_15Test -34: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) -34: [----------] 1 test from FFTTest (3 ms total) -34: -34: [----------] 10 tests from 7_8_25_36_60/FFTTest1D -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) -34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 -34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (10 ms) -34: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (26 ms total) -34: -34: [----------] 2 tests from Works/ParameterizedFFTTest3D -34: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 -34: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) -34: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 -34: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) -34: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) -34: -34: [----------] Global test environment tear-down -34: [==========] 15 tests from 4 test suites ran. (50 ms total) -34: [ PASSED ] 15 tests. -34/96 Test #34: FFTUnitTests ................................. Passed 0.26 sec -test 35 - Start 35: GpuUtilsUnitTests - -35: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" -35: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gpu_utils/tests -35: Test timeout computed to be: 30 -35: [==========] Running 67 tests from 22 test suites. -35: [----------] Global test environment set-up. -35: [----------] 2 tests from ClfftInitializer -35: [ RUN ] ClfftInitializer.SingleInitializationWorks -35: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) -35: [ RUN ] ClfftInitializer.TwoInitializationsWork -35: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) -35: [----------] 2 tests from ClfftInitializer (0 ms total) -35: -35: [----------] 1 test from DevicesAvailable -35: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice -35: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) -35: [----------] 1 test from DevicesAvailable (0 ms total) -35: -35: [----------] 1 test from DeviceStreamManagerTest -35: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice -35: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) -35: [----------] 1 test from DeviceStreamManagerTest (0 ms total) -35: -35: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int -35: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks -35: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory -35: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) -35: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) -35: -35: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float -35: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks -35: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory -35: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) -35: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) -35: -35: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector -35: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks -35: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory -35: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) -35: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) -35: -35: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly -35: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks -35: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory -35: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) -35: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int -35: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks -35: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork -35: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve -35: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) -35: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float -35: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks -35: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork -35: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve -35: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) -35: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector -35: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks -35: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork -35: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) -35: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve -35: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) -35: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) -35: -35: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int -35: [ RUN ] HostAllocatorTestNoMem/0.CreateVector -35: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment -35: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction -35: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/0.Swap -35: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/0.Comparison -35: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) -35: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) -35: -35: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float -35: [ RUN ] HostAllocatorTestNoMem/1.CreateVector -35: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment -35: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction -35: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/1.Swap -35: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/1.Comparison -35: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) -35: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) -35: -35: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector -35: [ RUN ] HostAllocatorTestNoMem/2.CreateVector -35: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment -35: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction -35: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/2.Swap -35: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/2.Comparison -35: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) -35: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) -35: -35: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly -35: [ RUN ] HostAllocatorTestNoMem/3.CreateVector -35: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment -35: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction -35: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/3.Swap -35: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) -35: [ RUN ] HostAllocatorTestNoMem/3.Comparison -35: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) -35: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int -35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment -35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction -35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float -35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment -35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction -35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) -35: -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector -35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment -35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction -35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) -35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator -35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) -35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) -35: -35: [----------] 1 test from HostAllocatorUntypedTest -35: [ RUN ] HostAllocatorUntypedTest.Comparison -35: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) -35: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) -35: -35: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator -35: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment -35: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment -35: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment -35: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/0.Move -35: [ OK ] AllocatorTest/0.Move (0 ms) -35: [----------] 4 tests from AllocatorTest/0 (0 ms total) -35: -35: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator -35: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment -35: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment -35: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment -35: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/1.Move -35: [ OK ] AllocatorTest/1.Move (0 ms) -35: [----------] 4 tests from AllocatorTest/1 (0 ms total) -35: -35: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> -35: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment -35: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment -35: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment -35: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/2.Move -35: [ OK ] AllocatorTest/2.Move (0 ms) -35: [----------] 4 tests from AllocatorTest/2 (0 ms total) -35: -35: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator -35: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment -35: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment -35: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment -35: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) -35: [ RUN ] AllocatorTest/3.Move -35: [ OK ] AllocatorTest/3.Move (0 ms) -35: [----------] 4 tests from AllocatorTest/3 (0 ms total) -35: -35: [----------] Global test environment tear-down -35: [==========] 67 tests from 22 test suites ran. (1 ms total) -35: [ PASSED ] 67 tests. -35/96 Test #35: GpuUtilsUnitTests ............................ Passed 0.22 sec -test 36 - Start 36: HardwareUnitTests - -36: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/HardwareUnitTests.xml" -36: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/hardware/tests -36: Test timeout computed to be: 30 -36: [==========] Running 22 tests from 10 test suites. -36: [----------] Global test environment set-up. -36: [----------] 1 test from CpuInfoTest -36: [ RUN ] CpuInfoTest.SupportLevel -36: [ OK ] CpuInfoTest.SupportLevel (1 ms) -36: [----------] 1 test from CpuInfoTest (1 ms total) -36: -36: [----------] 4 tests from HardwareTopologyTest -36: [ RUN ] HardwareTopologyTest.Execute -36: [ OK ] HardwareTopologyTest.Execute (18 ms) -36: [ RUN ] HardwareTopologyTest.HwlocExecute -36: [ OK ] HardwareTopologyTest.HwlocExecute (14 ms) -36: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency -36: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (16 ms) -36: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency -36: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (18 ms) -36: [----------] 4 tests from HardwareTopologyTest (68 ms total) -36: -36: [----------] 1 test from DevicesManagerTest -36: [ RUN ] DevicesManagerTest.Serialization -36: [ OK ] DevicesManagerTest.Serialization (0 ms) -36: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid -36: [----------] 1 test from DevicesManagerTest (0 ms total) -36: -36: [----------] 1 test from UuidStringTest -36: [ RUN ] UuidStringTest.Works -36: [ OK ] UuidStringTest.Works (0 ms) -36: [----------] 1 test from UuidStringTest (0 ms total) -36: -36: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest -36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 -36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 -36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 -36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 -36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 -36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -36: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) -36: -36: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest -36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 -36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 -36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 -36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) -36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 -36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) -36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 -36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) -36: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) -36: -36: [----------] 2 tests from Core12900K/MockHardwareTopologyTest -36: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 -36: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) -36: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 -36: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) -36: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) -36: -36: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest -36: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -36: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) -36: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) -36: -36: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest -36: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -36: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -36: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) -36: -36: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest -36: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 -36: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) -36: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (1 ms total) -36: -36: [----------] Global test environment tear-down -36: [==========] 22 tests from 10 test suites ran. (81 ms total) -36: [ PASSED ] 22 tests. -36: -36: YOU HAVE 1 DISABLED TEST -36: -36/96 Test #36: HardwareUnitTests ............................ Passed 0.27 sec -test 37 - Start 37: MathUnitTests - -37: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MathUnitTests.xml" -37: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/math/tests -37: Test timeout computed to be: 30 -37: [==========] Running 328 tests from 41 test suites. -37: [----------] Global test environment set-up. -37: [----------] 1 test from EmptyArrayRefWithPaddingTest -37: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty -37: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) -37: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) -37: -37: [----------] 1 test from EmptyConstArrayRefWithPaddingTest -37: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty -37: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) -37: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) -37: -37: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding -37: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks -37: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) -37: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks -37: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) -37: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) -37: -37: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding -37: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks -37: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) -37: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks -37: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) -37: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) -37: -37: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding -37: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks -37: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) -37: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks -37: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) -37: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) -37: -37: [----------] 2 tests from InvertBoxMatrixTest -37: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent -37: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) -37: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace -37: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) -37: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) -37: -37: [----------] 8 tests from ComplexNumberTest -37: [ RUN ] ComplexNumberTest.RealComplexMultiply -37: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) -37: [ RUN ] ComplexNumberTest.RealComplexExp -37: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexAdd -37: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexSubtract -37: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexMultiply -37: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexDivision -37: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexConjugate -37: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) -37: [ RUN ] ComplexNumberTest.ComplexAbs2 -37: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) -37: [----------] 8 tests from ComplexNumberTest (0 ms total) -37: -37: [----------] 11 tests from TranslateAndScaleTest -37: [ RUN ] TranslateAndScaleTest.identityTransformation -37: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) -37: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling -37: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation -37: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) -37: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial -37: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) -37: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector -37: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingIdentity -37: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingNonTrivial -37: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector -37: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero -37: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero -37: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) -37: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector -37: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) -37: [----------] 11 tests from TranslateAndScaleTest (0 ms total) -37: -37: [----------] 3 tests from AffineTransformationTest -37: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors -37: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) -37: [ RUN ] AffineTransformationTest.applyTransformationToVectors -37: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) -37: [ RUN ] AffineTransformationTest.retrieveGradient -37: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) -37: [----------] 3 tests from AffineTransformationTest (0 ms total) -37: -37: [----------] 14 tests from DensitySimilarityTest -37: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect -37: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect -37: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch -37: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) -37: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch -37: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) -37: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect -37: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero -37: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) -37: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect -37: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect -37: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne -37: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (18 ms) -37: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated -37: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (17 ms) -37: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated -37: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) -37: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect -37: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.NormalizationCorrect -37: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) -37: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive -37: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) -37: [----------] 14 tests from DensitySimilarityTest (37 ms total) -37: -37: [----------] 6 tests from StructureSimilarityTest -37: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD -37: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) -37: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho -37: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) -37: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD -37: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) -37: [ RUN ] StructureSimilarityTest.YieldsCorrectRho -37: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) -37: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex -37: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) -37: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex -37: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) -37: [----------] 6 tests from StructureSimilarityTest (0 ms total) -37: -37: [----------] 8 tests from ExponentialMovingAverage -37: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero -37: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) -37: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative -37: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) -37: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue -37: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) -37: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue -37: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) -37: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly -37: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) -37: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing -37: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) -37: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect -37: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) -37: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree -37: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) -37: [----------] 8 tests from ExponentialMovingAverage (0 ms total) -37: -37: [----------] 21 tests from FunctionTest -37: [ RUN ] FunctionTest.StaticLog2 -37: [ OK ] FunctionTest.StaticLog2 (0 ms) -37: [ RUN ] FunctionTest.Log2I32Bit -37: [ OK ] FunctionTest.Log2I32Bit (0 ms) -37: [ RUN ] FunctionTest.Log2I64Bit -37: [ OK ] FunctionTest.Log2I64Bit (0 ms) -37: [ RUN ] FunctionTest.GreatestCommonDivisor -37: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) -37: [ RUN ] FunctionTest.InvsqrtFloat -37: [ OK ] FunctionTest.InvsqrtFloat (0 ms) -37: [ RUN ] FunctionTest.InvsqrtDouble -37: [ OK ] FunctionTest.InvsqrtDouble (0 ms) -37: [ RUN ] FunctionTest.InvsqrtInteger -37: [ OK ] FunctionTest.InvsqrtInteger (0 ms) -37: [ RUN ] FunctionTest.InvcbrtFloat -37: [ OK ] FunctionTest.InvcbrtFloat (0 ms) -37: [ RUN ] FunctionTest.InvcbrtDouble -37: [ OK ] FunctionTest.InvcbrtDouble (0 ms) -37: [ RUN ] FunctionTest.InvcbrtInteger -37: [ OK ] FunctionTest.InvcbrtInteger (0 ms) -37: [ RUN ] FunctionTest.SixthrootFloat -37: [ OK ] FunctionTest.SixthrootFloat (0 ms) -37: [ RUN ] FunctionTest.SixthrootDouble -37: [ OK ] FunctionTest.SixthrootDouble (0 ms) -37: [ RUN ] FunctionTest.SixthrootInteger -37: [ OK ] FunctionTest.SixthrootInteger (0 ms) -37: [ RUN ] FunctionTest.InvsixthrootFloat -37: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) -37: [ RUN ] FunctionTest.InvsixthrootDouble -37: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) -37: [ RUN ] FunctionTest.InvsixthrootInteger -37: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) -37: [ RUN ] FunctionTest.Powers -37: [ OK ] FunctionTest.Powers (0 ms) -37: [ RUN ] FunctionTest.ErfInvFloat -37: [ OK ] FunctionTest.ErfInvFloat (0 ms) -37: [ RUN ] FunctionTest.ErfInvDouble -37: [ OK ] FunctionTest.ErfInvDouble (0 ms) -37: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat -37: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) -37: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble -37: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) -37: [----------] 21 tests from FunctionTest (2 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char -37: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char -37: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short -37: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short -37: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int -37: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int -37: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long -37: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) -37: -37: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long -37: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo -37: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) -37: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp -37: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) -37: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) -37: -37: [----------] 4 tests from GaussianOn1DLattice -37: [ RUN ] GaussianOn1DLattice.sumsCloseToOne -37: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) -37: [ RUN ] GaussianOn1DLattice.isCorrect -37: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) -37: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero -37: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) -37: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange -37: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) -37: [----------] 4 tests from GaussianOn1DLattice (0 ms total) -37: -37: [----------] 9 tests from GaussTransformTest -37: [ RUN ] GaussTransformTest.isZeroUponConstruction -37: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) -37: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss -37: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) -37: [ RUN ] GaussTransformTest.isZeroAfterSettingZero -37: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) -37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX -37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) -37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY -37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) -37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ -37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) -37: [ RUN ] GaussTransformTest.complementaryGaussAddToZero -37: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) -37: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues -37: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) -37: [ RUN ] GaussTransformTest.view -37: [ OK ] GaussTransformTest.view (0 ms) -37: [----------] 9 tests from GaussTransformTest (0 ms total) -37: -37: [----------] 3 tests from DensityFittingForce -37: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity -37: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) -37: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections -37: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) -37: [ RUN ] DensityFittingForce.pullsTowardsDerivative -37: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) -37: [----------] 3 tests from DensityFittingForce (0 ms total) -37: -37: [----------] 2 tests from InvertMatrixTest -37: [ RUN ] InvertMatrixTest.IdentityIsImpotent -37: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) -37: [ RUN ] InvertMatrixTest.ComputesInverse -37: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) -37: [----------] 2 tests from InvertMatrixTest (0 ms total) -37: -37: [----------] 22 tests from MatrixTest -37: [ RUN ] MatrixTest.canSetFromArray -37: [ OK ] MatrixTest.canSetFromArray (0 ms) -37: [ RUN ] MatrixTest.canSetStaticallyFromList -37: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) -37: [ RUN ] MatrixTest.canConstructAndFill -37: [ OK ] MatrixTest.canConstructAndFill (0 ms) -37: [ RUN ] MatrixTest.canSetValues -37: [ OK ] MatrixTest.canSetValues (0 ms) -37: [ RUN ] MatrixTest.canCopyAssign -37: [ OK ] MatrixTest.canCopyAssign (0 ms) -37: [ RUN ] MatrixTest.canSwap -37: [ OK ] MatrixTest.canSwap (0 ms) -37: [ RUN ] MatrixTest.staticMultiDimArrayExtent -37: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) -37: [ RUN ] MatrixTest.canAddMatrix -37: [ OK ] MatrixTest.canAddMatrix (0 ms) -37: [ RUN ] MatrixTest.canSubstractMatrix -37: [ OK ] MatrixTest.canSubstractMatrix (0 ms) -37: [ RUN ] MatrixTest.canNegateMatrix -37: [ OK ] MatrixTest.canNegateMatrix (0 ms) -37: [ RUN ] MatrixTest.determinantWorks -37: [ OK ] MatrixTest.determinantWorks (0 ms) -37: [ RUN ] MatrixTest.noninvertableDeterminantIsZero -37: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) -37: [ RUN ] MatrixTest.determinantOfDiagonalMatrix -37: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) -37: [ RUN ] MatrixTest.traceWorks -37: [ OK ] MatrixTest.traceWorks (0 ms) -37: [ RUN ] MatrixTest.transposeWorks -37: [ OK ] MatrixTest.transposeWorks (0 ms) -37: [ RUN ] MatrixTest.transposeOfSymmetricMatrix -37: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) -37: [ RUN ] MatrixTest.canCreateFromLegacyMatrix -37: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) -37: [ RUN ] MatrixTest.canFillLegacyMatrix -37: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) -37: [ RUN ] MatrixTest.IdentityMatrix -37: [ OK ] MatrixTest.IdentityMatrix (0 ms) -37: [ RUN ] MatrixTest.MatrixMatrixInnerProduct -37: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) -37: [ RUN ] MatrixTest.MatrixMatrixMultiplication -37: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) -37: [ RUN ] MatrixTest.MatrixVectorMultiplication -37: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) -37: [----------] 22 tests from MatrixTest (0 ms total) -37: -37: [----------] 25 tests from MultiDimArrayTest -37: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic -37: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic -37: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canSetValuesInStatic -37: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic -37: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canMoveConstructStatic -37: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic -37: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canMoveAssignStatic -37: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic -37: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canCopyConstructStatic -37: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic -37: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canCopyAssignStatic -37: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic -37: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.canSwapStatic -37: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) -37: [ RUN ] MultiDimArrayTest.canSwapDynamic -37: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) -37: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent -37: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) -37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent -37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) -37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent -37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) -37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue -37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) -37: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray -37: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) -37: [ RUN ] MultiDimArrayTest.conversionToView -37: [ OK ] MultiDimArrayTest.conversionToView (0 ms) -37: [ RUN ] MultiDimArrayTest.conversionToConstView -37: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) -37: [ RUN ] MultiDimArrayTest.viewBegin -37: [ OK ] MultiDimArrayTest.viewBegin (0 ms) -37: [ RUN ] MultiDimArrayTest.viewEnd -37: [ OK ] MultiDimArrayTest.viewEnd (0 ms) -37: [ RUN ] MultiDimArrayTest.constViewConstBegin -37: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) -37: [ RUN ] MultiDimArrayTest.constViewConstEnd -37: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) -37: [----------] 25 tests from MultiDimArrayTest (0 ms total) -37: -37: [----------] 4 tests from MultiDimArrayToMdSpanTest -37: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan -37: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) -37: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan -37: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) -37: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan -37: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) -37: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan -37: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) -37: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) -37: -37: [----------] 9 tests from NelderMeadSimplexTest -37: [ RUN ] NelderMeadSimplexTest.BestVertex -37: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) -37: [ RUN ] NelderMeadSimplexTest.WorstVertex -37: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) -37: [ RUN ] NelderMeadSimplexTest.SecondWorstValue -37: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) -37: [ RUN ] NelderMeadSimplexTest.ReflectionPoint -37: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) -37: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint -37: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) -37: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint -37: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) -37: [ RUN ] NelderMeadSimplexTest.SwapOutWorst -37: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) -37: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest -37: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) -37: [ RUN ] NelderMeadSimplexTest.OrientedLength -37: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) -37: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) -37: -37: [----------] 2 tests from NelderMead -37: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly -37: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) -37: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly -37: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) -37: [----------] 2 tests from NelderMead (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator -37: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.ResizeWorks -37: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.ReserveWorks -37: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/0.CanCopyAssign -37: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/0.CanMoveAssign -37: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/0.CanSwap -37: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator -37: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.ResizeWorks -37: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.ReserveWorks -37: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/1.CanCopyAssign -37: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/1.CanMoveAssign -37: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/1.CanSwap -37: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator -37: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.ResizeWorks -37: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.ReserveWorks -37: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/2.CanCopyAssign -37: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/2.CanMoveAssign -37: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/2.CanSwap -37: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > -37: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.ResizeWorks -37: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.ReserveWorks -37: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/3.CanCopyAssign -37: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/3.CanMoveAssign -37: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/3.CanSwap -37: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > -37: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.ResizeWorks -37: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.ReserveWorks -37: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/4.CanCopyAssign -37: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/4.CanMoveAssign -37: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/4.CanSwap -37: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator -37: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.ResizeWorks -37: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.ReserveWorks -37: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/5.CanCopyAssign -37: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/5.CanMoveAssign -37: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/5.CanSwap -37: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator -37: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.ResizeWorks -37: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.ReserveWorks -37: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/6.CanCopyAssign -37: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/6.CanMoveAssign -37: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/6.CanSwap -37: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator -37: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.ResizeWorks -37: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.ReserveWorks -37: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/7.CanCopyAssign -37: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/7.CanMoveAssign -37: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/7.CanSwap -37: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -37: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.ResizeWorks -37: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.ReserveWorks -37: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/8.CanCopyAssign -37: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/8.CanMoveAssign -37: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/8.CanSwap -37: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) -37: -37: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> -37: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks -37: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.ResizeWorks -37: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.ReserveWorks -37: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve -37: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) -37: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks -37: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks -37: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks -37: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) -37: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical -37: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) -37: [ RUN ] PaddedVectorTest/9.CanCopyAssign -37: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) -37: [ RUN ] PaddedVectorTest/9.CanMoveAssign -37: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) -37: [ RUN ] PaddedVectorTest/9.CanSwap -37: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) -37: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) -37: -37: [----------] 41 tests from RVecTest -37: [ RUN ] RVecTest.CanBeStoredInVector -37: [ OK ] RVecTest.CanBeStoredInVector (0 ms) -37: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec -37: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) -37: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec -37: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) -37: [ RUN ] RVecTest.WorksAsMutable_rvec -37: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) -37: [ RUN ] RVecTest.WorksAs_rvec_Array -37: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) -37: [ RUN ] RVecTest.ComparesEqual -37: [ OK ] RVecTest.ComparesEqual (0 ms) -37: [ RUN ] RVecTest.ComparesUnequal -37: [ OK ] RVecTest.ComparesUnequal (0 ms) -37: [ RUN ] RVecTest.CanAddRVecToRvec -37: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) -37: [ RUN ] RVecTest.CanAddAssignRVecToRvec -37: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) -37: [ RUN ] RVecTest.CanSubtractRVecFromRvec -37: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) -37: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec -37: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) -37: [ RUN ] RVecTest.CanDotProductRVecByRvec -37: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) -37: [ RUN ] RVecTest.CanCrossProductRVecByRvec -37: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) -37: [ RUN ] RVecTest.CanDivideRVecInplace -37: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) -37: [ RUN ] RVecTest.CanScaleRVec -37: [ OK ] RVecTest.CanScaleRVec (0 ms) -37: [ RUN ] RVecTest.CanDivideRVec -37: [ OK ] RVecTest.CanDivideRVec (0 ms) -37: [ RUN ] RVecTest.CanDoUnitvFromRVec -37: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) -37: [ RUN ] RVecTest.CanSqLengthOfRVec -37: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) -37: [ RUN ] RVecTest.CanLengthOfRVec -37: [ OK ] RVecTest.CanLengthOfRVec (0 ms) -37: [ RUN ] RVecTest.CanCastToRVec -37: [ OK ] RVecTest.CanCastToRVec (0 ms) -37: [ RUN ] RVecTest.CanCastToDVec -37: [ OK ] RVecTest.CanCastToDVec (0 ms) -37: [ RUN ] RVecTest.CanLeftScalarMultiply -37: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) -37: [ RUN ] RVecTest.CanRightScalarMultiply -37: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) -37: [ RUN ] RVecTest.CanGetUnitvFromRVec -37: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) -37: [ RUN ] RVecTest.CanGetSqLengthOfRVec -37: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) -37: [ RUN ] RVecTest.CanGetLengthOfRVec -37: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) -37: [ RUN ] RVecTest.CanDoCrossProductOfRVec -37: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) -37: [ RUN ] RVecTest.CanDoDotProductOfRVec -37: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) -37: [ RUN ] RVecTest.CanScaleByVector -37: [ OK ] RVecTest.CanScaleByVector (0 ms) -37: [ RUN ] RVecTest.CanNegate -37: [ OK ] RVecTest.CanNegate (0 ms) -37: [ RUN ] RVecTest.asIVec -37: [ OK ] RVecTest.asIVec (0 ms) -37: [ RUN ] RVecTest.elementWiseMin -37: [ OK ] RVecTest.elementWiseMin (0 ms) -37: [ RUN ] RVecTest.elementWiseMax -37: [ OK ] RVecTest.elementWiseMax (0 ms) -37: [ RUN ] RVecTest.WorksAs_dvec_Reference -37: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) -37: [ RUN ] RVecTest.WorksAs_ivec_Reference -37: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) -37: [ RUN ] RVecTest.WorksAs_rvec_Reference -37: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) -37: [ RUN ] RVecTest.CopyConstructorWorks -37: [ OK ] RVecTest.CopyConstructorWorks (0 ms) -37: [ RUN ] RVecTest.CopyAssignmentWorks -37: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) -37: [ RUN ] RVecTest.MoveConstructorWorks -37: [ OK ] RVecTest.MoveConstructorWorks (0 ms) -37: [ RUN ] RVecTest.MoveAssignmentWorks -37: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) -37: [ RUN ] RVecTest.UsableInConstexpr -37: [ OK ] RVecTest.UsableInConstexpr (0 ms) -37: [----------] 41 tests from RVecTest (0 ms total) -37: -37: [----------] Global test environment tear-down -37: [==========] 328 tests from 41 test suites ran. (43 ms total) -37: [ PASSED ] 328 tests. -37/96 Test #37: MathUnitTests ................................ Passed 0.24 sec -test 38 - Start 38: MdrunUtilityUnitTests - -38: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" -38: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests -38: Test timeout computed to be: 30 -38: [==========] Running 21 tests from 2 test suites. -38: [----------] Global test environment set-up. -38: [----------] 4 tests from MDModulesNotifierTest -38: [ RUN ] MDModulesNotifierTest.AddConsumer -38: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) -38: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter -38: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) -38: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers -38: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) -38: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources -38: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) -38: [----------] 4 tests from MDModulesNotifierTest (0 ms total) -38: -38: [----------] 17 tests from ThreadAffinityTest -38: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled -38: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported -38: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads -38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads -38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads -38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware -38: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads -38: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset -38: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) -38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride -38: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto -38: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced -38: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced -38: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) -38: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread -38: NOTE: Affinity setting failed. -38: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto -38: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced -38: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) -38: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads -38: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) -38: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing -38: NOTE: Affinity setting for 1/2 threads failed. -38: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) -38: [----------] 17 tests from ThreadAffinityTest (2 ms total) -38: -38: [----------] Global test environment tear-down -38: [==========] 21 tests from 2 test suites ran. (2 ms total) -38: [ PASSED ] 21 tests. -38/96 Test #38: MdrunUtilityUnitTests ........................ Passed 0.20 sec -test 39 - Start 39: MdrunUtilityMpiUnitTests - -39: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" -39: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdrunutility/tests -39: Test timeout computed to be: 30 -39: [==========] Running 13 tests from 2 test suites. -39: [----------] Global test environment set-up. -39: [----------] 6 tests from ThreadAffinityMultiRankTest -39: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode -39: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (0 ms) -39: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride -39: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) -39: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes -39: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) -39: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled -39: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) -39: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto -39: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) -39: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce -39: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) -39: [----------] 6 tests from ThreadAffinityMultiRankTest (1 ms total) -39: -39: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) -39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly -39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) -39: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (1 ms total) -39: -39: [----------] Global test environment tear-down -39: [==========] 13 tests from 2 test suites ran. (3 ms total) -39: [ PASSED ] 13 tests. -39/96 Test #39: MdrunUtilityMpiUnitTests ..................... Passed 0.28 sec -test 40 - Start 40: MDSpanTests - -40: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MDSpanTests.xml" -40: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdspan/tests -40: Test timeout computed to be: 30 -40: [==========] Running 32 tests from 7 test suites. -40: [----------] Global test environment set-up. -40: [----------] 4 tests from BasicAccessorPolicy -40: [ RUN ] BasicAccessorPolicy.Decay -40: [ OK ] BasicAccessorPolicy.Decay (0 ms) -40: [ RUN ] BasicAccessorPolicy.Access -40: [ OK ] BasicAccessorPolicy.Access (0 ms) -40: [ RUN ] BasicAccessorPolicy.Offset -40: [ OK ] BasicAccessorPolicy.Offset (0 ms) -40: [ RUN ] BasicAccessorPolicy.CopyAccessor -40: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) -40: [----------] 4 tests from BasicAccessorPolicy (0 ms total) -40: -40: [----------] 4 tests from ExtentsTest -40: [ RUN ] ExtentsTest.Construction -40: [ OK ] ExtentsTest.Construction (0 ms) -40: [ RUN ] ExtentsTest.PurelyStatic -40: [ OK ] ExtentsTest.PurelyStatic (0 ms) -40: [ RUN ] ExtentsTest.RankNought -40: [ OK ] ExtentsTest.RankNought (0 ms) -40: [ RUN ] ExtentsTest.Assignment -40: [ OK ] ExtentsTest.Assignment (0 ms) -40: [----------] 4 tests from ExtentsTest (0 ms total) -40: -40: [----------] 8 tests from MdSpanExtension -40: [ RUN ] MdSpanExtension.SlicingAllStatic -40: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) -40: [ RUN ] MdSpanExtension.SlicingDynamic -40: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) -40: [ RUN ] MdSpanExtension.SlicingAllStatic3D -40: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) -40: [ RUN ] MdSpanExtension.SlicingEqualsView3D -40: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) -40: [ RUN ] MdSpanExtension.additionWorks -40: [ OK ] MdSpanExtension.additionWorks (0 ms) -40: [ RUN ] MdSpanExtension.subtractionWorks -40: [ OK ] MdSpanExtension.subtractionWorks (0 ms) -40: [ RUN ] MdSpanExtension.multiplicationWorks -40: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) -40: [ RUN ] MdSpanExtension.divisionWorks -40: [ OK ] MdSpanExtension.divisionWorks (0 ms) -40: [----------] 8 tests from MdSpanExtension (0 ms total) -40: -40: [----------] 3 tests from LayoutTests -40: [ RUN ] LayoutTests.LayoutRightConstruction -40: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) -40: [ RUN ] LayoutTests.LayoutRightProperties -40: [ OK ] LayoutTests.LayoutRightProperties (0 ms) -40: [ RUN ] LayoutTests.LayoutRightOperator -40: [ OK ] LayoutTests.LayoutRightOperator (0 ms) -40: [----------] 3 tests from LayoutTests (0 ms total) -40: -40: [----------] 1 test from MdSpanTest -40: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly -40: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) -40: [----------] 1 test from MdSpanTest (0 ms total) -40: -40: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -40: [ RUN ] MdSpanTest/0.Rank -40: [ OK ] MdSpanTest/0.Rank (0 ms) -40: [ RUN ] MdSpanTest/0.DynamicRank -40: [ OK ] MdSpanTest/0.DynamicRank (0 ms) -40: [ RUN ] MdSpanTest/0.Extents -40: [ OK ] MdSpanTest/0.Extents (0 ms) -40: [ RUN ] MdSpanTest/0.Strides -40: [ OK ] MdSpanTest/0.Strides (0 ms) -40: [ RUN ] MdSpanTest/0.Properties -40: [ OK ] MdSpanTest/0.Properties (0 ms) -40: [ RUN ] MdSpanTest/0.Operator -40: [ OK ] MdSpanTest/0.Operator (0 ms) -40: [----------] 6 tests from MdSpanTest/0 (0 ms total) -40: -40: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > -40: [ RUN ] MdSpanTest/1.Rank -40: [ OK ] MdSpanTest/1.Rank (0 ms) -40: [ RUN ] MdSpanTest/1.DynamicRank -40: [ OK ] MdSpanTest/1.DynamicRank (0 ms) -40: [ RUN ] MdSpanTest/1.Extents -40: [ OK ] MdSpanTest/1.Extents (0 ms) -40: [ RUN ] MdSpanTest/1.Strides -40: [ OK ] MdSpanTest/1.Strides (0 ms) -40: [ RUN ] MdSpanTest/1.Properties -40: [ OK ] MdSpanTest/1.Properties (0 ms) -40: [ RUN ] MdSpanTest/1.Operator -40: [ OK ] MdSpanTest/1.Operator (0 ms) -40: [----------] 6 tests from MdSpanTest/1 (0 ms total) -40: -40: [----------] Global test environment tear-down -40: [==========] 32 tests from 7 test suites ran. (0 ms total) -40: [ PASSED ] 32 tests. -40/96 Test #40: MDSpanTests .................................. Passed 0.19 sec -test 41 - Start 41: MdtypesUnitTest - -41: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" -41: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/mdtypes/tests -41: Test timeout computed to be: 30 -41: [==========] Running 97 tests from 7 test suites. -41: [----------] Global test environment set-up. -41: [----------] 4 tests from ForeingLambdaTermsDhdl -41: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks -41: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) -41: [ RUN ] ForeingLambdaTermsDhdl.AllLinear -41: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) -41: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative -41: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) -41: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul -41: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) -41: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) -41: -41: [----------] 4 tests from ObservablesReducerTest -41: [ RUN ] ObservablesReducerTest.CanMoveAssign -41: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) -41: [ RUN ] ObservablesReducerTest.CanMoveConstruct -41: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) -41: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers -41: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) -41: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber -41: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) -41: [----------] 4 tests from ObservablesReducerTest (0 ms total) -41: -41: [----------] 2 tests from CheckpointDataTest -41: [ RUN ] CheckpointDataTest.SingleDataTest -41: [ OK ] CheckpointDataTest.SingleDataTest (10 ms) -41: [ RUN ] CheckpointDataTest.MultiDataTest -41: [ OK ] CheckpointDataTest.MultiDataTest (58 ms) -41: [----------] 2 tests from CheckpointDataTest (69 ms total) -41: -41: [----------] 7 tests from ForceBuffers -41: [ RUN ] ForceBuffers.ConstructsUnpinned -41: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) -41: [ RUN ] ForceBuffers.ConstructsPinned -41: [ OK ] ForceBuffers.ConstructsPinned (0 ms) -41: [ RUN ] ForceBuffers.ConstructsEmpty -41: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) -41: [ RUN ] ForceBuffers.ResizeWorks -41: [ OK ] ForceBuffers.ResizeWorks (0 ms) -41: [ RUN ] ForceBuffers.PaddingWorks -41: [ OK ] ForceBuffers.PaddingWorks (0 ms) -41: [ RUN ] ForceBuffers.CopyWorks -41: [ OK ] ForceBuffers.CopyWorks (0 ms) -41: [ RUN ] ForceBuffers.CopyDoesNotPin -41: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) -41: [----------] 7 tests from ForceBuffers (0 ms total) -41: -41: [----------] 5 tests from MultipleTimeStepping -41: [ RUN ] MultipleTimeStepping.ChecksNumLevels -41: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) -41: [ RUN ] MultipleTimeStepping.SelectsForceGroups -41: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) -41: [ RUN ] MultipleTimeStepping.ChecksStepFactor -41: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) -41: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel -41: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) -41: [ RUN ] MultipleTimeStepping.ChecksIntegrator -41: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) -41: [----------] 5 tests from MultipleTimeStepping (0 ms total) -41: -41: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) -41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 -41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) -41: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) -41: -41: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) -41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 -41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) -41: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) -41: -41: [----------] Global test environment tear-down -41: [==========] 97 tests from 7 test suites ran. (71 ms total) -41: [ PASSED ] 97 tests. -41/96 Test #41: MdtypesUnitTest .............................. Passed 0.26 sec -test 42 - Start 42: OnlineHelpUnitTests - -42: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" -42: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/onlinehelp/tests -42: Test timeout computed to be: 30 -42: [==========] Running 22 tests from 4 test suites. -42: [----------] Global test environment set-up. -42: [----------] 6 tests from TextTableFormatterTest -42: [ RUN ] TextTableFormatterTest.HandlesBasicCase -42: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) -42: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles -42: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) -42: [ RUN ] TextTableFormatterTest.HandlesIndentation -42: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) -42: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines -42: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) -42: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding -42: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) -42: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns -42: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) -42: [----------] 6 tests from TextTableFormatterTest (0 ms total) -42: -42: [----------] 3 tests from HelpManagerTest -42: [ RUN ] HelpManagerTest.HandlesRootTopic -42: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) -42: [ RUN ] HelpManagerTest.HandlesSubTopics -42: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) -42: [ RUN ] HelpManagerTest.HandlesInvalidTopics -42: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) -42: [----------] 3 tests from HelpManagerTest (0 ms total) -42: -42: [----------] 2 tests from HelpTopicFormattingTest -42: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic -42: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) -42: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics -42: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) -42: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) -42: -42: [----------] 11 tests from HelpWriterContextTest -42: [ RUN ] HelpWriterContextTest.FormatsParagraphs -42: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs -42: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) -42: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace -42: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsLiteralText -42: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning -42: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation -42: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsBulletList -42: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList -42: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsSimpleTable -42: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsGridTable -42: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) -42: [ RUN ] HelpWriterContextTest.FormatsTitles -42: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) -42: [----------] 11 tests from HelpWriterContextTest (0 ms total) -42: -42: [----------] Global test environment tear-down -42: [==========] 22 tests from 4 test suites ran. (2 ms total) -42: [ PASSED ] 22 tests. -42/96 Test #42: OnlineHelpUnitTests .......................... Passed 0.19 sec -test 43 - Start 43: OptionsUnitTests - -43: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/OptionsUnitTests.xml" -43: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/tests -43: Test timeout computed to be: 30 -43: [==========] Running 112 tests from 18 test suites. -43: [----------] Global test environment set-up. -43: [----------] 5 tests from AbstractOptionStorageTest -43: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish -43: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) -43: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval -43: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) -43: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition -43: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) -43: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition -43: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) -43: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues -43: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) -43: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) -43: -43: [----------] 10 tests from FileNameOptionTest -43: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension -43: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue -43: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption -43: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension -43: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension -43: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension -43: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) -43: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix -43: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) -43: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix -43: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension -43: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) -43: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue -43: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) -43: [----------] 10 tests from FileNameOptionTest (0 ms total) -43: -43: [----------] 16 tests from FileNameOptionManagerTest -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension -43: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) -43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile -43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile -43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile -43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile -43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified -43: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified -43: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified -43: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile -43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) -43: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking -43: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) -43: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile -43: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) -43: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) -43: -43: [----------] 1 test from OptionsTest -43: [ RUN ] OptionsTest.FailsOnNonsafeStorage -43: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) -43: [----------] 1 test from OptionsTest (0 ms total) -43: -43: [----------] 9 tests from OptionsAssignerTest -43: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter -43: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue -43: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter -43: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter -43: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesMissingValue -43: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesExtraValue -43: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesGroups -43: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesSections -43: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) -43: [ RUN ] OptionsAssignerTest.HandlesMultipleSources -43: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) -43: [----------] 9 tests from OptionsAssignerTest (0 ms total) -43: -43: [----------] 4 tests from OptionsAssignerBooleanTest -43: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue -43: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) -43: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue -43: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) -43: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo -43: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) -43: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue -43: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) -43: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) -43: -43: [----------] 13 tests from OptionsAssignerIntegerTest -43: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue -43: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue -43: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue -43: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow -43: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue -43: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet -43: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet -43: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues -43: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.StoresToVector -43: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors -43: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue -43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue -43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) -43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment -43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) -43: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) -43: -43: [----------] 5 tests from OptionsAssignerDoubleTest -43: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue -43: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) -43: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat -43: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) -43: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue -43: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) -43: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue -43: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) -43: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue -43: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) -43: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) -43: -43: [----------] 9 tests from OptionsAssignerStringTest -43: [ RUN ] OptionsAssignerStringTest.StoresSingleValue -43: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue -43: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray -43: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue -43: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue -43: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue -43: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue -43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable -43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) -43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector -43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) -43: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) -43: -43: [----------] 6 tests from OptionsAssignerEnumTest -43: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue -43: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) -43: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues -43: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) -43: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange -43: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) -43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue -43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) -43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable -43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) -43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector -43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) -43: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) -43: -43: [----------] 8 tests from RepeatingOptionSectionTest -43: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance -43: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption -43: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance -43: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue -43: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances -43: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault -43: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault -43: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) -43: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections -43: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) -43: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) -43: -43: [----------] 1 test from TimeUnitManagerTest -43: [ RUN ] TimeUnitManagerTest.BasicOperations -43: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) -43: [----------] 1 test from TimeUnitManagerTest (0 ms total) -43: -43: [----------] 4 tests from TimeUnitBehaviorTest -43: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue -43: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) -43: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues -43: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) -43: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources -43: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) -43: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks -43: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) -43: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) -43: -43: [----------] 2 tests from TreeValueSupportAssignTest -43: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree -43: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) -43: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays -43: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) -43: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) -43: -43: [----------] 1 test from TreeValueSupportAssignErrorTest -43: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue -43: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) -43: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) -43: -43: [----------] 5 tests from TreeValueSupportCheckTest -43: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty -43: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) -43: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree -43: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) -43: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 -43: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) -43: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 -43: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) -43: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue -43: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) -43: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) -43: -43: [----------] 6 tests from TreeValueSupportAdjustTest -43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues -43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) -43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues -43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) -43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues -43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) -43: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues -43: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) -43: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues -43: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) -43: [ RUN ] TreeValueSupportAdjustTest.OrdersValues -43: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) -43: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) -43: -43: [----------] 7 tests from TreeValueSupportTest -43: [ RUN ] TreeValueSupportTest.SupportsBooleanOption -43: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsIntegerOption -43: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsInt64Option -43: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsStringOption -43: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsFloatOption -43: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsDoubleOption -43: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) -43: [ RUN ] TreeValueSupportTest.SupportsEnumOption -43: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) -43: [----------] 7 tests from TreeValueSupportTest (0 ms total) -43: -43: [----------] Global test environment tear-down -43: [==========] 112 tests from 18 test suites ran. (4 ms total) -43: [ PASSED ] 112 tests. -43/96 Test #43: OptionsUnitTests ............................. Passed 0.20 sec -test 44 - Start 44: PbcutilUnitTest - -44: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" -44: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pbcutil/tests -44: Test timeout computed to be: 30 -44: [==========] Running 37 tests from 5 test suites. -44: [----------] Global test environment set-up. -44: [----------] 1 test from ShiftTest -44: [ RUN ] ShiftTest.CoordinateShiftWorks -44: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) -44: [----------] 1 test from ShiftTest (0 ms total) -44: -44: [----------] 2 tests from MShift -44: [ RUN ] MShift.shiftsAndUnshifts -44: [ OK ] MShift.shiftsAndUnshifts (0 ms) -44: [ RUN ] MShift.shiftsAndUnshiftsSelf -44: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) -44: [----------] 2 tests from MShift (0 ms total) -44: -44: [----------] 5 tests from PbcTest -44: [ RUN ] PbcTest.CalcShiftsWorks -44: [ OK ] PbcTest.CalcShiftsWorks (0 ms) -44: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox -44: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) -44: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox -44: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) -44: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox -44: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) -44: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf -44: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) -44: [----------] 5 tests from PbcTest (0 ms total) -44: -44: [----------] 2 tests from PbcEnumsTest -44: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect -44: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) -44: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect -44: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) -44: [----------] 2 tests from PbcEnumsTest (0 ms total) -44: -44: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) -44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 -44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) -44: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (6 ms total) -44: -44: [----------] Global test environment tear-down -44: [==========] 37 tests from 5 test suites ran. (7 ms total) -44: [ PASSED ] 37 tests. -44/96 Test #44: PbcutilUnitTest .............................. Passed 0.20 sec -test 45 - Start 45: RandomUnitTests - -45: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/RandomUnitTests.xml" -45: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/random/tests -45: Test timeout computed to be: 30 -45: [==========] Running 44 tests from 10 test suites. -45: [----------] Global test environment set-up. -45: [----------] 4 tests from ExponentialDistributionTest -45: [ RUN ] ExponentialDistributionTest.Output -45: [ OK ] ExponentialDistributionTest.Output (0 ms) -45: [ RUN ] ExponentialDistributionTest.Logical -45: [ OK ] ExponentialDistributionTest.Logical (0 ms) -45: [ RUN ] ExponentialDistributionTest.Reset -45: [ OK ] ExponentialDistributionTest.Reset (0 ms) -45: [ RUN ] ExponentialDistributionTest.AltParam -45: [ OK ] ExponentialDistributionTest.AltParam (0 ms) -45: [----------] 4 tests from ExponentialDistributionTest (0 ms total) -45: -45: [----------] 4 tests from GammaDistributionTest -45: [ RUN ] GammaDistributionTest.Output -45: [ OK ] GammaDistributionTest.Output (0 ms) -45: [ RUN ] GammaDistributionTest.Logical -45: [ OK ] GammaDistributionTest.Logical (0 ms) -45: [ RUN ] GammaDistributionTest.Reset -45: [ OK ] GammaDistributionTest.Reset (0 ms) -45: [ RUN ] GammaDistributionTest.AltParam -45: [ OK ] GammaDistributionTest.AltParam (0 ms) -45: [----------] 4 tests from GammaDistributionTest (0 ms total) -45: -45: [----------] 4 tests from NormalDistributionTest -45: [ RUN ] NormalDistributionTest.Output -45: [ OK ] NormalDistributionTest.Output (0 ms) -45: [ RUN ] NormalDistributionTest.Logical -45: [ OK ] NormalDistributionTest.Logical (0 ms) -45: [ RUN ] NormalDistributionTest.Reset -45: [ OK ] NormalDistributionTest.Reset (0 ms) -45: [ RUN ] NormalDistributionTest.AltParam -45: [ OK ] NormalDistributionTest.AltParam (0 ms) -45: [----------] 4 tests from NormalDistributionTest (0 ms total) -45: -45: [----------] 1 test from SeedTest -45: [ RUN ] SeedTest.makeRandomSeed -45: [ OK ] SeedTest.makeRandomSeed (0 ms) -45: [----------] 1 test from SeedTest (0 ms total) -45: -45: [----------] 6 tests from TabulatedNormalDistributionTest -45: [ RUN ] TabulatedNormalDistributionTest.Output14 -45: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) -45: [ RUN ] TabulatedNormalDistributionTest.Output16 -45: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) -45: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 -45: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) -45: [ RUN ] TabulatedNormalDistributionTest.Logical -45: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) -45: [ RUN ] TabulatedNormalDistributionTest.Reset -45: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) -45: [ RUN ] TabulatedNormalDistributionTest.AltParam -45: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) -45: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) -45: -45: [----------] 1 test from TabulatedNormalDistributionTableTest -45: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties -45: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) -45: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) -45: -45: [----------] 6 tests from ThreeFry2x64Test -45: [ RUN ] ThreeFry2x64Test.Logical -45: [ OK ] ThreeFry2x64Test.Logical (0 ms) -45: [ RUN ] ThreeFry2x64Test.InternalCounterSequence -45: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) -45: [ RUN ] ThreeFry2x64Test.Reseed -45: [ OK ] ThreeFry2x64Test.Reseed (0 ms) -45: [ RUN ] ThreeFry2x64Test.Discard -45: [ OK ] ThreeFry2x64Test.Discard (0 ms) -45: [ RUN ] ThreeFry2x64Test.InvalidCounter -45: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) -45: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter -45: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) -45: [----------] 6 tests from ThreeFry2x64Test (0 ms total) -45: -45: [----------] 4 tests from UniformIntDistributionTest -45: [ RUN ] UniformIntDistributionTest.Output -45: [ OK ] UniformIntDistributionTest.Output (0 ms) -45: [ RUN ] UniformIntDistributionTest.Logical -45: [ OK ] UniformIntDistributionTest.Logical (0 ms) -45: [ RUN ] UniformIntDistributionTest.Reset -45: [ OK ] UniformIntDistributionTest.Reset (0 ms) -45: [ RUN ] UniformIntDistributionTest.AltParam -45: [ OK ] UniformIntDistributionTest.AltParam (0 ms) -45: [----------] 4 tests from UniformIntDistributionTest (0 ms total) -45: -45: [----------] 5 tests from UniformRealDistributionTest -45: [ RUN ] UniformRealDistributionTest.GenerateCanonical -45: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) -45: [ RUN ] UniformRealDistributionTest.Output -45: [ OK ] UniformRealDistributionTest.Output (0 ms) -45: [ RUN ] UniformRealDistributionTest.Logical -45: [ OK ] UniformRealDistributionTest.Logical (0 ms) -45: [ RUN ] UniformRealDistributionTest.Reset -45: [ OK ] UniformRealDistributionTest.Reset (0 ms) -45: [ RUN ] UniformRealDistributionTest.AltParam -45: [ OK ] UniformRealDistributionTest.AltParam (0 ms) -45: [----------] 5 tests from UniformRealDistributionTest (0 ms total) -45: -45: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) -45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 -45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) -45: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) -45: -45: [----------] Global test environment tear-down -45: [==========] 44 tests from 10 test suites ran. (2 ms total) -45: [ PASSED ] 44 tests. -45/96 Test #45: RandomUnitTests .............................. Passed 0.43 sec -test 46 - Start 46: RestraintTests - -46: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/RestraintTests.xml" -46: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/restraint/tests -46: Test timeout computed to be: 30 -46: [==========] Running 1 test from 1 test suite. -46: [----------] Global test environment set-up. -46: [----------] 1 test from RestraintManager -46: [ RUN ] RestraintManager.restraintList -46: [ OK ] RestraintManager.restraintList (0 ms) -46: [----------] 1 test from RestraintManager (0 ms total) -46: -46: [----------] Global test environment tear-down -46: [==========] 1 test from 1 test suite ran. (0 ms total) -46: [ PASSED ] 1 test. -46/96 Test #46: RestraintTests ............................... Passed 0.44 sec -test 47 - Start 47: TableUnitTests - -47: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TableUnitTests.xml" -47: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tables/tests -47: Test timeout computed to be: 30 -47: [==========] Running 20 tests from 2 test suites. -47: [----------] Global test environment set-up. -47: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable -47: [ RUN ] SplineTableTest/0.HandlesIncorrectInput -47: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) -47: [ RUN ] SplineTableTest/0.Sinc -47: [ OK ] SplineTableTest/0.Sinc (0 ms) -47: [ RUN ] SplineTableTest/0.LJ12 -47: [ OK ] SplineTableTest/0.LJ12 (6 ms) -47: [ RUN ] SplineTableTest/0.PmeCorrection -47: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) -47: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput -47: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) -47: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr -47: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) -47: [ RUN ] SplineTableTest/0.TwoFunctions -47: [ OK ] SplineTableTest/0.TwoFunctions (11 ms) -47: [ RUN ] SplineTableTest/0.ThreeFunctions -47: [ OK ] SplineTableTest/0.ThreeFunctions (12 ms) -47: [ RUN ] SplineTableTest/0.Simd -47: [ OK ] SplineTableTest/0.Simd (2 ms) -47: [ RUN ] SplineTableTest/0.SimdTwoFunctions -47: [ OK ] SplineTableTest/0.SimdTwoFunctions (11 ms) -47: [----------] 10 tests from SplineTableTest/0 (46 ms total) -47: -47: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable -47: [ RUN ] SplineTableTest/1.HandlesIncorrectInput -47: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) -47: [ RUN ] SplineTableTest/1.Sinc -47: [ OK ] SplineTableTest/1.Sinc (0 ms) -47: [ RUN ] SplineTableTest/1.LJ12 -47: [ OK ] SplineTableTest/1.LJ12 (0 ms) -47: [ RUN ] SplineTableTest/1.PmeCorrection -47: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) -47: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput -47: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) -47: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr -47: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) -47: [ RUN ] SplineTableTest/1.TwoFunctions -47: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) -47: [ RUN ] SplineTableTest/1.ThreeFunctions -47: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) -47: [ RUN ] SplineTableTest/1.Simd -47: [ OK ] SplineTableTest/1.Simd (0 ms) -47: [ RUN ] SplineTableTest/1.SimdTwoFunctions -47: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) -47: [----------] 10 tests from SplineTableTest/1 (8 ms total) -47: -47: [----------] Global test environment tear-down -47: [==========] 20 tests from 2 test suites ran. (55 ms total) -47: [ PASSED ] 20 tests. -47/96 Test #47: TableUnitTests ............................... Passed 0.25 sec -test 48 - Start 48: TaskAssignmentUnitTests - -48: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" -48: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/taskassignment/tests -48: Test timeout computed to be: 30 -48: [==========] Running 3 tests from 2 test suites. -48: [----------] Global test environment set-up. -48: [----------] 2 tests from UserTaskAssignmentStringHandlingTest -48: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork -48: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) -48: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid -48: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) -48: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) -48: -48: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest -48: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow -48: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) -48: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) -48: -48: [----------] Global test environment tear-down -48: [==========] 3 tests from 2 test suites ran. (0 ms total) -48: [ PASSED ] 3 tests. -48/96 Test #48: TaskAssignmentUnitTests ...................... Passed 0.19 sec -test 49 - Start 49: GmxTimingTests - -49: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxTimingTests.xml" -49: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/timing/tests -49: Test timeout computed to be: 30 -49: [==========] Running 6 tests from 1 test suite. -49: [----------] Global test environment set-up. -49: [----------] 6 tests from TimingTest -49: [ RUN ] TimingTest.ElementCountingWorks -49: [ OK ] TimingTest.ElementCountingWorks (0 ms) -49: [ RUN ] TimingTest.ElementNoCountingWorks -49: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) -49: [ RUN ] TimingTest.SubElementCountingWorks -49: [ OK ] TimingTest.SubElementCountingWorks (0 ms) -49: [ RUN ] TimingTest.SubElementNoCountingWorks -49: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) -49: [ RUN ] TimingTest.RunWallCycle -49: [ OK ] TimingTest.RunWallCycle (1 ms) -49: [ RUN ] TimingTest.RunWallCycleSub -49: [ OK ] TimingTest.RunWallCycleSub (0 ms) -49: [----------] 6 tests from TimingTest (1 ms total) -49: -49: [----------] Global test environment tear-down -49: [==========] 6 tests from 1 test suite ran. (1 ms total) -49: [ PASSED ] 6 tests. -49/96 Test #49: GmxTimingTests ............................... Passed 0.19 sec -test 50 - Start 50: TopologyTest - -50: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TopologyTest.xml" -50: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/topology/tests -50: Test timeout computed to be: 30 -50: [==========] Running 153 tests from 10 test suites. -50: [----------] Global test environment set-up. -50: [----------] 3 tests from PdbAtomEntryTest -50: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry -50: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) -50: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac -50: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) -50: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry -50: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) -50: [----------] 3 tests from PdbAtomEntryTest (0 ms total) -50: -50: [----------] 3 tests from ExclusionBlockTest -50: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks -50: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) -50: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka -50: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) -50: [ RUN ] ExclusionBlockTest.MergeExclusions -50: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) -50: [----------] 3 tests from ExclusionBlockTest (0 ms total) -50: -50: [----------] 6 tests from InteractionListTest -50: [ RUN ] InteractionListTest.EmptyWorks -50: [ OK ] InteractionListTest.EmptyWorks (0 ms) -50: [ RUN ] InteractionListTest.CanAddInteractionArray -50: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) -50: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms -50: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) -50: [ RUN ] InteractionListTest.CanAddInteractionPointer -50: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) -50: [ RUN ] InteractionListTest.CanAddListToOtherList -50: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) -50: [ RUN ] InteractionListTest.ClearingWorks -50: [ OK ] InteractionListTest.ClearingWorks (0 ms) -50: [----------] 6 tests from InteractionListTest (0 ms total) -50: -50: [----------] 3 tests from IndexTest -50: [ RUN ] IndexTest.AnalyseWorksDefaultGroups -50: -50: WARNING: Masses and atomic (Van der Waals) radii will be guessed -50: based on residue and atom names, since they could not be -50: definitively assigned from the information in your input -50: files. These guessed numbers might deviate from the mass -50: and radius of the atom type. Please check the output -50: files if necessary. Note, that this functionality may -50: be removed in a future GROMACS version. Please, consider -50: using another file format for your input. -50: -50: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) -50: [ RUN ] IndexTest.WriteIndexWorks -50: -50: WARNING: Masses and atomic (Van der Waals) radii will be guessed -50: based on residue and atom names, since they could not be -50: definitively assigned from the information in your input -50: files. These guessed numbers might deviate from the mass -50: and radius of the atom type. Please check the output -50: files if necessary. Note, that this functionality may -50: be removed in a future GROMACS version. Please, consider -50: using another file format for your input. -50: -50: [ OK ] IndexTest.WriteIndexWorks (11 ms) -50: [ RUN ] IndexTest.WriteAndReadIndexWorks -50: -50: WARNING: Masses and atomic (Van der Waals) radii will be guessed -50: based on residue and atom names, since they could not be -50: definitively assigned from the information in your input -50: files. These guessed numbers might deviate from the mass -50: and radius of the atom type. Please check the output -50: files if necessary. Note, that this functionality may -50: be removed in a future GROMACS version. Please, consider -50: using another file format for your input. -50: -50: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) -50: [----------] 3 tests from IndexTest (15 ms total) -50: -50: [----------] 4 tests from MtopTest -50: [ RUN ] MtopTest.RangeBasedLoop -50: [ OK ] MtopTest.RangeBasedLoop (0 ms) -50: [ RUN ] MtopTest.Operators -50: [ OK ] MtopTest.Operators (0 ms) -50: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms -50: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) -50: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly -50: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) -50: [----------] 4 tests from MtopTest (0 ms total) -50: -50: [----------] 2 tests from IListRangeTest -50: [ RUN ] IListRangeTest.RangeBasedLoopWorks -50: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) -50: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction -50: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) -50: [----------] 2 tests from IListRangeTest (0 ms total) -50: -50: [----------] 13 tests from StringTableTest -50: [ RUN ] StringTableTest.AddSingleEntry -50: [ OK ] StringTableTest.AddSingleEntry (0 ms) -50: [ RUN ] StringTableTest.CanAccessWithAt -50: [ OK ] StringTableTest.CanAccessWithAt (0 ms) -50: [ RUN ] StringTableTest.CanAccessWithBracket -50: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) -50: [ RUN ] StringTableTest.ThrowsOutOfRange -50: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) -50: [ RUN ] StringTableTest.StringCompareIsCorrect -50: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) -50: [ RUN ] StringTableTest.AddTwoDistinctEntries -50: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) -50: [ RUN ] StringTableTest.TryToAddDuplicates -50: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) -50: [ RUN ] StringTableTest.AddLargeNumberOfEntries -50: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) -50: [ RUN ] StringTableTest.NoDuplicatesInLargeTable -50: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) -50: [ RUN ] StringTableTest.CanWriteToBuffer -50: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) -50: [ RUN ] StringTableTest.Roundtrip -50: [ OK ] StringTableTest.Roundtrip (0 ms) -50: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices -50: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) -50: [ RUN ] StringTableTest.CanCopyToLegacyTable -50: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) -50: [----------] 13 tests from StringTableTest (2 ms total) -50: -50: [----------] 6 tests from LegacySymtabTest -50: [ RUN ] LegacySymtabTest.EmptyOnOpen -50: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) -50: [ RUN ] LegacySymtabTest.AddSingleEntry -50: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) -50: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries -50: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) -50: [ RUN ] LegacySymtabTest.TryToAddDuplicates -50: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) -50: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries -50: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) -50: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable -50: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) -50: [----------] 6 tests from LegacySymtabTest (0 ms total) -50: -50: [----------] 5 tests from TopSortTest -50: [ RUN ] TopSortTest.WorksOnEmptyIdef -50: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) -50: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction -50: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) -50: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions -50: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) -50: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions -50: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) -50: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions -50: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) -50: [----------] 5 tests from TopSortTest (0 ms total) -50: -50: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) -50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 -50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) -50: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (9 ms total) -50: -50: [----------] Global test environment tear-down -50: [==========] 153 tests from 10 test suites ran. (27 ms total) -50: [ PASSED ] 153 tests. -50: -50: YOU HAVE 1 DISABLED TEST -50: -50/96 Test #50: TopologyTest ................................. Passed 0.22 sec -test 51 - Start 51: PullTest - -51: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/PullTest.xml" -51: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pulling/tests -51: Test timeout computed to be: 30 -51: [==========] Running 10 tests from 1 test suite. -51: [----------] Global test environment set-up. -51: [----------] 10 tests from PullTest -51: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox -51: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) -51: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox -51: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) -51: [ RUN ] PullTest.MaxPullDistanceXyzTricBox -51: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) -51: [ RUN ] PullTest.MaxPullDistanceXyzLongBox -51: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) -51: [ RUN ] PullTest.MaxPullDistanceXySkewedBox -51: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) -51: [ RUN ] PullTest.TransformationCoordSimple -51: [ OK ] PullTest.TransformationCoordSimple (0 ms) -51: [ RUN ] PullTest.TransformationCoordAdvanced -51: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) -51: [ RUN ] PullTest.TransformationCoordTime -51: [ OK ] PullTest.TransformationCoordTime (0 ms) -51: [ RUN ] PullTest.TransformationCoordTimeNotAllowed -51: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) -51: [ RUN ] PullTest.TransformationCoordDummyExpression -51: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) -51: [----------] 10 tests from PullTest (0 ms total) -51: -51: [----------] Global test environment tear-down -51: [==========] 10 tests from 1 test suite ran. (0 ms total) -51: [ PASSED ] 10 tests. -51/96 Test #51: PullTest ..................................... Passed 0.20 sec -test 52 - Start 52: SimdUnitTests - -52: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/SimdUnitTests.xml" -52: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/simd/tests -52: Test timeout computed to be: 30 -52: [==========] Running 288 tests from 22 test suites. -52: [----------] Global test environment set-up. -52: [----------] 9 tests from SimdBootstrapTest -52: [ RUN ] SimdBootstrapTest.loadStore -52: [ OK ] SimdBootstrapTest.loadStore (0 ms) -52: [ RUN ] SimdBootstrapTest.loadU -52: [ OK ] SimdBootstrapTest.loadU (0 ms) -52: [ RUN ] SimdBootstrapTest.storeU -52: [ OK ] SimdBootstrapTest.storeU (0 ms) -52: [ RUN ] SimdBootstrapTest.loadStoreI -52: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) -52: [ RUN ] SimdBootstrapTest.loadUI -52: [ OK ] SimdBootstrapTest.loadUI (0 ms) -52: [ RUN ] SimdBootstrapTest.storeUI -52: [ OK ] SimdBootstrapTest.storeUI (0 ms) -52: [ RUN ] SimdBootstrapTest.simd4LoadStore -52: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) -52: [ RUN ] SimdBootstrapTest.simd4LoadU -52: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) -52: [ RUN ] SimdBootstrapTest.simd4StoreU -52: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) -52: [----------] 9 tests from SimdBootstrapTest (0 ms total) -52: -52: [----------] 41 tests from SimdScalarTest -52: [ RUN ] SimdScalarTest.load -52: [ OK ] SimdScalarTest.load (0 ms) -52: [ RUN ] SimdScalarTest.loadU -52: [ OK ] SimdScalarTest.loadU (0 ms) -52: [ RUN ] SimdScalarTest.store -52: [ OK ] SimdScalarTest.store (0 ms) -52: [ RUN ] SimdScalarTest.storeU -52: [ OK ] SimdScalarTest.storeU (0 ms) -52: [ RUN ] SimdScalarTest.setZero -52: [ OK ] SimdScalarTest.setZero (0 ms) -52: [ RUN ] SimdScalarTest.andNot -52: [ OK ] SimdScalarTest.andNot (0 ms) -52: [ RUN ] SimdScalarTest.fma -52: [ OK ] SimdScalarTest.fma (0 ms) -52: [ RUN ] SimdScalarTest.fms -52: [ OK ] SimdScalarTest.fms (0 ms) -52: [ RUN ] SimdScalarTest.fnma -52: [ OK ] SimdScalarTest.fnma (0 ms) -52: [ RUN ] SimdScalarTest.fnms -52: [ OK ] SimdScalarTest.fnms (0 ms) -52: [ RUN ] SimdScalarTest.maskAdd -52: [ OK ] SimdScalarTest.maskAdd (0 ms) -52: [ RUN ] SimdScalarTest.maskzMul -52: [ OK ] SimdScalarTest.maskzMul (0 ms) -52: [ RUN ] SimdScalarTest.maskzFma -52: [ OK ] SimdScalarTest.maskzFma (0 ms) -52: [ RUN ] SimdScalarTest.abs -52: [ OK ] SimdScalarTest.abs (0 ms) -52: [ RUN ] SimdScalarTest.max -52: [ OK ] SimdScalarTest.max (0 ms) -52: [ RUN ] SimdScalarTest.min -52: [ OK ] SimdScalarTest.min (0 ms) -52: [ RUN ] SimdScalarTest.round -52: [ OK ] SimdScalarTest.round (0 ms) -52: [ RUN ] SimdScalarTest.trunc -52: [ OK ] SimdScalarTest.trunc (0 ms) -52: [ RUN ] SimdScalarTest.reduce -52: [ OK ] SimdScalarTest.reduce (0 ms) -52: [ RUN ] SimdScalarTest.testBits -52: [ OK ] SimdScalarTest.testBits (0 ms) -52: [ RUN ] SimdScalarTest.anyTrue -52: [ OK ] SimdScalarTest.anyTrue (0 ms) -52: [ RUN ] SimdScalarTest.selectByMask -52: [ OK ] SimdScalarTest.selectByMask (0 ms) -52: [ RUN ] SimdScalarTest.selectByNotMask -52: [ OK ] SimdScalarTest.selectByNotMask (0 ms) -52: [ RUN ] SimdScalarTest.blend -52: [ OK ] SimdScalarTest.blend (0 ms) -52: [ RUN ] SimdScalarTest.cvtR2I -52: [ OK ] SimdScalarTest.cvtR2I (0 ms) -52: [ RUN ] SimdScalarTest.cvttR2I -52: [ OK ] SimdScalarTest.cvttR2I (0 ms) -52: [ RUN ] SimdScalarTest.cvtI2R -52: [ OK ] SimdScalarTest.cvtI2R (0 ms) -52: [ RUN ] SimdScalarTest.cvtF2D -52: [ OK ] SimdScalarTest.cvtF2D (0 ms) -52: [ RUN ] SimdScalarTest.cvtD2D -52: [ OK ] SimdScalarTest.cvtD2D (0 ms) -52: [ RUN ] SimdScalarTest.loadI -52: [ OK ] SimdScalarTest.loadI (0 ms) -52: [ RUN ] SimdScalarTest.loadUI -52: [ OK ] SimdScalarTest.loadUI (0 ms) -52: [ RUN ] SimdScalarTest.storeI -52: [ OK ] SimdScalarTest.storeI (0 ms) -52: [ RUN ] SimdScalarTest.storeUI -52: [ OK ] SimdScalarTest.storeUI (0 ms) -52: [ RUN ] SimdScalarTest.andNotI -52: [ OK ] SimdScalarTest.andNotI (0 ms) -52: [ RUN ] SimdScalarTest.testBitsI -52: [ OK ] SimdScalarTest.testBitsI (0 ms) -52: [ RUN ] SimdScalarTest.selectByMaskI -52: [ OK ] SimdScalarTest.selectByMaskI (0 ms) -52: [ RUN ] SimdScalarTest.selectByNotMaskI -52: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) -52: [ RUN ] SimdScalarTest.blendI -52: [ OK ] SimdScalarTest.blendI (0 ms) -52: [ RUN ] SimdScalarTest.cvtB2IB -52: [ OK ] SimdScalarTest.cvtB2IB (0 ms) -52: [ RUN ] SimdScalarTest.cvtIB2B -52: [ OK ] SimdScalarTest.cvtIB2B (0 ms) -52: [ RUN ] SimdScalarTest.expandScalarsToTriplets -52: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) -52: [----------] 41 tests from SimdScalarTest (0 ms total) -52: -52: [----------] 8 tests from SimdScalarUtilTest -52: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose -52: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) -52: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose -52: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) -52: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU -52: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) -52: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU -52: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) -52: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU -52: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) -52: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose -52: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) -52: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose -52: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) -52: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum -52: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) -52: [----------] 8 tests from SimdScalarUtilTest (0 ms total) -52: -52: [----------] 37 tests from SimdScalarMathTest -52: [ RUN ] SimdScalarMathTest.copysign -52: [ OK ] SimdScalarMathTest.copysign (0 ms) -52: [ RUN ] SimdScalarMathTest.invsqrtPair -52: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) -52: [ RUN ] SimdScalarMathTest.inv -52: [ OK ] SimdScalarMathTest.inv (0 ms) -52: [ RUN ] SimdScalarMathTest.maskzInvsqrt -52: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) -52: [ RUN ] SimdScalarMathTest.log -52: [ OK ] SimdScalarMathTest.log (0 ms) -52: [ RUN ] SimdScalarMathTest.exp2 -52: [ OK ] SimdScalarMathTest.exp2 (0 ms) -52: [ RUN ] SimdScalarMathTest.exp -52: [ OK ] SimdScalarMathTest.exp (0 ms) -52: [ RUN ] SimdScalarMathTest.erf -52: [ OK ] SimdScalarMathTest.erf (0 ms) -52: [ RUN ] SimdScalarMathTest.erfc -52: [ OK ] SimdScalarMathTest.erfc (0 ms) -52: [ RUN ] SimdScalarMathTest.sincos -52: [ OK ] SimdScalarMathTest.sincos (0 ms) -52: [ RUN ] SimdScalarMathTest.sin -52: [ OK ] SimdScalarMathTest.sin (0 ms) -52: [ RUN ] SimdScalarMathTest.cos -52: [ OK ] SimdScalarMathTest.cos (0 ms) -52: [ RUN ] SimdScalarMathTest.tan -52: [ OK ] SimdScalarMathTest.tan (0 ms) -52: [ RUN ] SimdScalarMathTest.asin -52: [ OK ] SimdScalarMathTest.asin (0 ms) -52: [ RUN ] SimdScalarMathTest.acos -52: [ OK ] SimdScalarMathTest.acos (0 ms) -52: [ RUN ] SimdScalarMathTest.atan -52: [ OK ] SimdScalarMathTest.atan (0 ms) -52: [ RUN ] SimdScalarMathTest.atan2 -52: [ OK ] SimdScalarMathTest.atan2 (0 ms) -52: [ RUN ] SimdScalarMathTest.pmeForceCorrection -52: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) -52: [ RUN ] SimdScalarMathTest.pmePotentialCorrection -52: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) -52: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy -52: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.invSingleAccuracy -52: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy -52: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.logSingleAccuracy -52: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy -52: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.expSingleAccuracy -52: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.erfSingleAccuracy -52: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy -52: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy -52: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.sinSingleAccuracy -52: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.cosSingleAccuracy -52: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.tanSingleAccuracy -52: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.asinSingleAccuracy -52: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.acosSingleAccuracy -52: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.atanSingleAccuracy -52: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy -52: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy -52: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -52: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy -52: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -52: [----------] 37 tests from SimdScalarMathTest (0 ms total) -52: -52: [----------] 1 test from SimdTest -52: [ RUN ] SimdTest.GmxAligned -52: [ OK ] SimdTest.GmxAligned (0 ms) -52: [----------] 1 test from SimdTest (0 ms total) -52: -52: [----------] 42 tests from SimdFloatingpointTest -52: [ RUN ] SimdFloatingpointTest.setZero -52: [ OK ] SimdFloatingpointTest.setZero (0 ms) -52: [ RUN ] SimdFloatingpointTest.set -52: [ OK ] SimdFloatingpointTest.set (0 ms) -52: [ RUN ] SimdFloatingpointTest.add -52: [ OK ] SimdFloatingpointTest.add (0 ms) -52: [ RUN ] SimdFloatingpointTest.maskAdd -52: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) -52: [ RUN ] SimdFloatingpointTest.sub -52: [ OK ] SimdFloatingpointTest.sub (0 ms) -52: [ RUN ] SimdFloatingpointTest.mul -52: [ OK ] SimdFloatingpointTest.mul (0 ms) -52: [ RUN ] SimdFloatingpointTest.maskzMul -52: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) -52: [ RUN ] SimdFloatingpointTest.fma -52: [ OK ] SimdFloatingpointTest.fma (0 ms) -52: [ RUN ] SimdFloatingpointTest.maskzFma -52: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) -52: [ RUN ] SimdFloatingpointTest.fms -52: [ OK ] SimdFloatingpointTest.fms (0 ms) -52: [ RUN ] SimdFloatingpointTest.fnma -52: [ OK ] SimdFloatingpointTest.fnma (0 ms) -52: [ RUN ] SimdFloatingpointTest.fnms -52: [ OK ] SimdFloatingpointTest.fnms (0 ms) -52: [ RUN ] SimdFloatingpointTest.abs -52: [ OK ] SimdFloatingpointTest.abs (0 ms) -52: [ RUN ] SimdFloatingpointTest.neg -52: [ OK ] SimdFloatingpointTest.neg (0 ms) -52: [ RUN ] SimdFloatingpointTest.and -52: [ OK ] SimdFloatingpointTest.and (0 ms) -52: [ RUN ] SimdFloatingpointTest.or -52: [ OK ] SimdFloatingpointTest.or (0 ms) -52: [ RUN ] SimdFloatingpointTest.xor -52: [ OK ] SimdFloatingpointTest.xor (0 ms) -52: [ RUN ] SimdFloatingpointTest.andNot -52: [ OK ] SimdFloatingpointTest.andNot (0 ms) -52: [ RUN ] SimdFloatingpointTest.max -52: [ OK ] SimdFloatingpointTest.max (0 ms) -52: [ RUN ] SimdFloatingpointTest.min -52: [ OK ] SimdFloatingpointTest.min (0 ms) -52: [ RUN ] SimdFloatingpointTest.round -52: [ OK ] SimdFloatingpointTest.round (0 ms) -52: [ RUN ] SimdFloatingpointTest.roundMode -52: [ OK ] SimdFloatingpointTest.roundMode (0 ms) -52: [ RUN ] SimdFloatingpointTest.trunc -52: [ OK ] SimdFloatingpointTest.trunc (0 ms) -52: [ RUN ] SimdFloatingpointTest.frexp -52: [ OK ] SimdFloatingpointTest.frexp (0 ms) -52: [ RUN ] SimdFloatingpointTest.ldexp -52: [ OK ] SimdFloatingpointTest.ldexp (0 ms) -52: [ RUN ] SimdFloatingpointTest.rsqrt -52: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) -52: [ RUN ] SimdFloatingpointTest.maskzRsqrt -52: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) -52: [ RUN ] SimdFloatingpointTest.rcp -52: [ OK ] SimdFloatingpointTest.rcp (0 ms) -52: [ RUN ] SimdFloatingpointTest.maskzRcp -52: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) -52: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask -52: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) -52: [ RUN ] SimdFloatingpointTest.selectByNotMask -52: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) -52: [ RUN ] SimdFloatingpointTest.cmpNe -52: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) -52: [ RUN ] SimdFloatingpointTest.cmpLe -52: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) -52: [ RUN ] SimdFloatingpointTest.cmpLt -52: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) -52: [ RUN ] SimdFloatingpointTest.testBits -52: [ OK ] SimdFloatingpointTest.testBits (0 ms) -52: [ RUN ] SimdFloatingpointTest.andB -52: [ OK ] SimdFloatingpointTest.andB (0 ms) -52: [ RUN ] SimdFloatingpointTest.orB -52: [ OK ] SimdFloatingpointTest.orB (0 ms) -52: [ RUN ] SimdFloatingpointTest.anyTrueB -52: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) -52: [ RUN ] SimdFloatingpointTest.blend -52: [ OK ] SimdFloatingpointTest.blend (0 ms) -52: [ RUN ] SimdFloatingpointTest.reduce -52: [ OK ] SimdFloatingpointTest.reduce (0 ms) -52: [ RUN ] SimdFloatingpointTest.cvtFloat2Double -52: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) -52: [ RUN ] SimdFloatingpointTest.cvtDouble2Float -52: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) -52: [----------] 42 tests from SimdFloatingpointTest (0 ms total) -52: -52: [----------] 16 tests from SimdFloatingpointUtilTest -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 -52: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 -52: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping -52: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 -52: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping -52: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets -52: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 -52: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum -52: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 -52: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN -52: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) -52: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset -52: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) -52: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) -52: -52: [----------] 23 tests from SimdIntegerTest -52: [ RUN ] SimdIntegerTest.setZero -52: [ OK ] SimdIntegerTest.setZero (0 ms) -52: [ RUN ] SimdIntegerTest.set -52: [ OK ] SimdIntegerTest.set (0 ms) -52: [ RUN ] SimdIntegerTest.add -52: [ OK ] SimdIntegerTest.add (0 ms) -52: [ RUN ] SimdIntegerTest.sub -52: [ OK ] SimdIntegerTest.sub (0 ms) -52: [ RUN ] SimdIntegerTest.mul -52: [ OK ] SimdIntegerTest.mul (0 ms) -52: [ RUN ] SimdIntegerTest.and -52: [ OK ] SimdIntegerTest.and (0 ms) -52: [ RUN ] SimdIntegerTest.andNot -52: [ OK ] SimdIntegerTest.andNot (0 ms) -52: [ RUN ] SimdIntegerTest.or -52: [ OK ] SimdIntegerTest.or (0 ms) -52: [ RUN ] SimdIntegerTest.xor -52: [ OK ] SimdIntegerTest.xor (0 ms) -52: [ RUN ] SimdIntegerTest.extract -52: [ OK ] SimdIntegerTest.extract (0 ms) -52: [ RUN ] SimdIntegerTest.cvtR2I -52: [ OK ] SimdIntegerTest.cvtR2I (0 ms) -52: [ RUN ] SimdIntegerTest.cvttR2I -52: [ OK ] SimdIntegerTest.cvttR2I (0 ms) -52: [ RUN ] SimdIntegerTest.cvtI2R -52: [ OK ] SimdIntegerTest.cvtI2R (0 ms) -52: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask -52: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) -52: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask -52: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) -52: [ RUN ] SimdIntegerTest.cmpLt -52: [ OK ] SimdIntegerTest.cmpLt (0 ms) -52: [ RUN ] SimdIntegerTest.testBits -52: [ OK ] SimdIntegerTest.testBits (0 ms) -52: [ RUN ] SimdIntegerTest.andB -52: [ OK ] SimdIntegerTest.andB (0 ms) -52: [ RUN ] SimdIntegerTest.orB -52: [ OK ] SimdIntegerTest.orB (0 ms) -52: [ RUN ] SimdIntegerTest.anyTrue -52: [ OK ] SimdIntegerTest.anyTrue (0 ms) -52: [ RUN ] SimdIntegerTest.blend -52: [ OK ] SimdIntegerTest.blend (0 ms) -52: [ RUN ] SimdIntegerTest.cvtB2IB -52: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) -52: [ RUN ] SimdIntegerTest.cvtIB2B -52: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) -52: [----------] 23 tests from SimdIntegerTest (0 ms total) -52: -52: [----------] 56 tests from SimdMathTest -52: [ RUN ] SimdMathTest.generateTestPointsFloat -52: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) -52: [ RUN ] SimdMathTest.copysign -52: [ OK ] SimdMathTest.copysign (0 ms) -52: [ RUN ] SimdMathTest.invsqrt -52: [ OK ] SimdMathTest.invsqrt (0 ms) -52: [ RUN ] SimdMathTest.maskzInvsqrt -52: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) -52: [ RUN ] SimdMathTest.invsqrtPair -52: [ OK ] SimdMathTest.invsqrtPair (0 ms) -52: [ RUN ] SimdMathTest.sqrt -52: [ OK ] SimdMathTest.sqrt (0 ms) -52: [ RUN ] SimdMathTest.sqrtUnsafe -52: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) -52: [ RUN ] SimdMathTest.inv -52: [ OK ] SimdMathTest.inv (1 ms) -52: [ RUN ] SimdMathTest.maskzInv -52: [ OK ] SimdMathTest.maskzInv (0 ms) -52: [ RUN ] SimdMathTest.cbrt -52: [ OK ] SimdMathTest.cbrt (0 ms) -52: [ RUN ] SimdMathTest.invcbrt -52: [ OK ] SimdMathTest.invcbrt (0 ms) -52: [ RUN ] SimdMathTest.log2 -52: [ OK ] SimdMathTest.log2 (0 ms) -52: [ RUN ] SimdMathTest.log -52: [ OK ] SimdMathTest.log (0 ms) -52: [ RUN ] SimdMathTest.exp2 -52: [ OK ] SimdMathTest.exp2 (0 ms) -52: [ RUN ] SimdMathTest.exp2Unsafe -52: [ OK ] SimdMathTest.exp2Unsafe (0 ms) -52: [ RUN ] SimdMathTest.exp -52: [ OK ] SimdMathTest.exp (0 ms) -52: [ RUN ] SimdMathTest.expUnsafe -52: [ OK ] SimdMathTest.expUnsafe (0 ms) -52: [ RUN ] SimdMathTest.pow -52: [ OK ] SimdMathTest.pow (0 ms) -52: [ RUN ] SimdMathTest.powUnsafe -52: [ OK ] SimdMathTest.powUnsafe (0 ms) -52: [ RUN ] SimdMathTest.erf -52: [ OK ] SimdMathTest.erf (0 ms) -52: [ RUN ] SimdMathTest.erfc -52: [ OK ] SimdMathTest.erfc (0 ms) -52: [ RUN ] SimdMathTest.sin -52: [ OK ] SimdMathTest.sin (0 ms) -52: [ RUN ] SimdMathTest.cos -52: [ OK ] SimdMathTest.cos (0 ms) -52: [ RUN ] SimdMathTest.tan -52: [ OK ] SimdMathTest.tan (0 ms) -52: [ RUN ] SimdMathTest.asin -52: [ OK ] SimdMathTest.asin (0 ms) -52: [ RUN ] SimdMathTest.acos -52: [ OK ] SimdMathTest.acos (0 ms) -52: [ RUN ] SimdMathTest.atan -52: [ OK ] SimdMathTest.atan (0 ms) -52: [ RUN ] SimdMathTest.atan2 -52: [ OK ] SimdMathTest.atan2 (0 ms) -52: [ RUN ] SimdMathTest.pmeForceCorrection -52: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) -52: [ RUN ] SimdMathTest.pmePotentialCorrection -52: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) -52: [ RUN ] SimdMathTest.invsqrtSingleAccuracy -52: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy -52: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.sqrtSingleAccuracy -52: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe -52: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) -52: [ RUN ] SimdMathTest.invSingleAccuracy -52: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) -52: [ RUN ] SimdMathTest.cbrtSingleAccuracy -52: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.invcbrtSingleAccuracy -52: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.log2SingleAccuracy -52: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.logSingleAccuracy -52: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.exp2SingleAccuracy -52: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe -52: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) -52: [ RUN ] SimdMathTest.expSingleAccuracy -52: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe -52: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) -52: [ RUN ] SimdMathTest.powSingleAccuracy -52: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe -52: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) -52: [ RUN ] SimdMathTest.erfSingleAccuracy -52: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.erfcSingleAccuracy -52: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.sinSingleAccuracy -52: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.cosSingleAccuracy -52: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.tanSingleAccuracy -52: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.asinSingleAccuracy -52: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.acosSingleAccuracy -52: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.atanSingleAccuracy -52: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.atan2SingleAccuracy -52: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy -52: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) -52: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy -52: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) -52: [----------] 56 tests from SimdMathTest (22 ms total) -52: -52: [----------] 1 test from EmptyArrayRefTest -52: [ RUN ] EmptyArrayRefTest.IsEmpty -52: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) -52: [----------] 1 test from EmptyArrayRefTest (0 ms total) -52: -52: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks -52: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) -52: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks -52: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) -52: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks -52: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) -52: [----------] 3 tests from ArrayRefTest/0 (0 ms total) -52: -52: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks -52: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) -52: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks -52: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) -52: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks -52: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) -52: [----------] 3 tests from ArrayRefTest/1 (0 ms total) -52: -52: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks -52: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) -52: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks -52: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) -52: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks -52: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) -52: [----------] 3 tests from ArrayRefTest/2 (0 ms total) -52: -52: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks -52: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) -52: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks -52: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) -52: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks -52: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) -52: [----------] 3 tests from ArrayRefTest/3 (0 ms total) -52: -52: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefReadWriteTest/0.Assignment -52: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) -52: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) -52: -52: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefReadWriteTest/1.Assignment -52: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) -52: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) -52: -52: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefArithmeticTest/0.Basic -52: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) -52: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) -52: -52: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef -52: [ RUN ] ArrayRefArithmeticTest/1.Basic -52: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) -52: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) -52: -52: [----------] 3 tests from SimdVectorOperationsTest -52: [ RUN ] SimdVectorOperationsTest.iprod -52: [ OK ] SimdVectorOperationsTest.iprod (0 ms) -52: [ RUN ] SimdVectorOperationsTest.norm2 -52: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) -52: [ RUN ] SimdVectorOperationsTest.cprod -52: [ OK ] SimdVectorOperationsTest.cprod (0 ms) -52: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) -52: -52: [----------] 32 tests from Simd4FloatingpointTest -52: [ RUN ] Simd4FloatingpointTest.setZero -52: [ OK ] Simd4FloatingpointTest.setZero (0 ms) -52: [ RUN ] Simd4FloatingpointTest.set -52: [ OK ] Simd4FloatingpointTest.set (0 ms) -52: [ RUN ] Simd4FloatingpointTest.add -52: [ OK ] Simd4FloatingpointTest.add (0 ms) -52: [ RUN ] Simd4FloatingpointTest.sub -52: [ OK ] Simd4FloatingpointTest.sub (0 ms) -52: [ RUN ] Simd4FloatingpointTest.mul -52: [ OK ] Simd4FloatingpointTest.mul (0 ms) -52: [ RUN ] Simd4FloatingpointTest.fma -52: [ OK ] Simd4FloatingpointTest.fma (0 ms) -52: [ RUN ] Simd4FloatingpointTest.fms -52: [ OK ] Simd4FloatingpointTest.fms (0 ms) -52: [ RUN ] Simd4FloatingpointTest.fnma -52: [ OK ] Simd4FloatingpointTest.fnma (0 ms) -52: [ RUN ] Simd4FloatingpointTest.fnms -52: [ OK ] Simd4FloatingpointTest.fnms (0 ms) -52: [ RUN ] Simd4FloatingpointTest.abs -52: [ OK ] Simd4FloatingpointTest.abs (0 ms) -52: [ RUN ] Simd4FloatingpointTest.neg -52: [ OK ] Simd4FloatingpointTest.neg (0 ms) -52: [ RUN ] Simd4FloatingpointTest.and -52: [ OK ] Simd4FloatingpointTest.and (0 ms) -52: [ RUN ] Simd4FloatingpointTest.or -52: [ OK ] Simd4FloatingpointTest.or (0 ms) -52: [ RUN ] Simd4FloatingpointTest.xor -52: [ OK ] Simd4FloatingpointTest.xor (0 ms) -52: [ RUN ] Simd4FloatingpointTest.andNot -52: [ OK ] Simd4FloatingpointTest.andNot (0 ms) -52: [ RUN ] Simd4FloatingpointTest.max -52: [ OK ] Simd4FloatingpointTest.max (0 ms) -52: [ RUN ] Simd4FloatingpointTest.min -52: [ OK ] Simd4FloatingpointTest.min (0 ms) -52: [ RUN ] Simd4FloatingpointTest.round -52: [ OK ] Simd4FloatingpointTest.round (0 ms) -52: [ RUN ] Simd4FloatingpointTest.trunc -52: [ OK ] Simd4FloatingpointTest.trunc (0 ms) -52: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR -52: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) -52: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask -52: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) -52: [ RUN ] Simd4FloatingpointTest.selectByNotMask -52: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) -52: [ RUN ] Simd4FloatingpointTest.cmpNe -52: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) -52: [ RUN ] Simd4FloatingpointTest.cmpLe -52: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) -52: [ RUN ] Simd4FloatingpointTest.cmpLt -52: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) -52: [ RUN ] Simd4FloatingpointTest.andB -52: [ OK ] Simd4FloatingpointTest.andB (0 ms) -52: [ RUN ] Simd4FloatingpointTest.orB -52: [ OK ] Simd4FloatingpointTest.orB (0 ms) -52: [ RUN ] Simd4FloatingpointTest.anyTrue -52: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) -52: [ RUN ] Simd4FloatingpointTest.blend -52: [ OK ] Simd4FloatingpointTest.blend (0 ms) -52: [ RUN ] Simd4FloatingpointTest.reduce -52: [ OK ] Simd4FloatingpointTest.reduce (0 ms) -52: [ RUN ] Simd4FloatingpointTest.dotProduct -52: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) -52: [ RUN ] Simd4FloatingpointTest.transpose -52: [ OK ] Simd4FloatingpointTest.transpose (0 ms) -52: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) -52: -52: [----------] 2 tests from Simd4MathTest -52: [ RUN ] Simd4MathTest.invsqrt -52: [ OK ] Simd4MathTest.invsqrt (0 ms) -52: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy -52: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) -52: [----------] 2 tests from Simd4MathTest (0 ms total) -52: -52: [----------] 1 test from Simd4VectorOperationsTest -52: [ RUN ] Simd4VectorOperationsTest.norm2 -52: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) -52: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) -52: -52: [----------] Global test environment tear-down -52: [==========] 288 tests from 22 test suites ran. (23 ms total) -52: [ PASSED ] 288 tests. -52/96 Test #52: SimdUnitTests ................................ Passed 0.28 sec -test 53 - Start 53: CompatibilityHelpersTests - -53: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" -53: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/compat/tests -53: Test timeout computed to be: 30 -53: [==========] Running 9 tests from 6 test suites. -53: [----------] Global test environment set-up. -53: [----------] 4 tests from TemplateMPTest -53: [ RUN ] TemplateMPTest.MpWithIndexInt -53: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) -53: [ RUN ] TemplateMPTest.MpWithIndexIntBad -53: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) -53: [ RUN ] TemplateMPTest.MpWithIndexBool -53: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) -53: [ RUN ] TemplateMPTest.MpWithIndexEnum -53: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) -53: [----------] 4 tests from TemplateMPTest (0 ms total) -53: -53: [----------] 1 test from NotNullConstruction -53: [ RUN ] NotNullConstruction.Works -53: [ OK ] NotNullConstruction.Works (0 ms) -53: [----------] 1 test from NotNullConstruction (0 ms total) -53: -53: [----------] 1 test from NotNullCasting -53: [ RUN ] NotNullCasting.Works -53: [ OK ] NotNullCasting.Works (0 ms) -53: [----------] 1 test from NotNullCasting (0 ms total) -53: -53: [----------] 1 test from NotNullAssignment -53: [ RUN ] NotNullAssignment.Works -53: [ OK ] NotNullAssignment.Works (0 ms) -53: [----------] 1 test from NotNullAssignment (0 ms total) -53: -53: [----------] 1 test from MakeNotNull -53: [ RUN ] MakeNotNull.Works -53: [ OK ] MakeNotNull.Works (0 ms) -53: [----------] 1 test from MakeNotNull (0 ms total) -53: -53: [----------] 1 test from NotNull -53: [ RUN ] NotNull.WorksInContainers -53: [ OK ] NotNull.WorksInContainers (0 ms) -53: [----------] 1 test from NotNull (0 ms total) -53: -53: [----------] Global test environment tear-down -53: [==========] 9 tests from 6 test suites ran. (0 ms total) -53: [ PASSED ] 9 tests. -53/96 Test #53: CompatibilityHelpersTests .................... Passed 0.27 sec -test 54 - Start 54: GmxAnaTest - -54: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxAnaTest.xml" -54: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxana/tests -54: Test timeout computed to be: 600 -54: [==========] Running 31 tests from 4 test suites. -54: [----------] Global test environment set-up. -54: [----------] 7 tests from Entropy -54: [ RUN ] Entropy.Schlitter_300_NoLinear -54: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) -54: [ RUN ] Entropy.Schlitter_300_Linear -54: [ OK ] Entropy.Schlitter_300_Linear (0 ms) -54: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear -54: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) -54: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear -54: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) -54: [ RUN ] Entropy.QuasiHarmonic_200_Linear -54: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) -54: [ RUN ] Entropy.EntropyCompare_200_Linear -54: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) -54: [ RUN ] Entropy.EntropyCompare_300_Linear -54: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) -54: [----------] 7 tests from Entropy (0 ms total) -54: -54: [----------] 2 tests from GmxChiTest -54: [ RUN ] GmxChiTest.gmxchiWorksWithAll -54: Analyzing from residue 1 to residue 11 -54: 10 residues with dihedrals found -54: 46 dihedrals found -54: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -54: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -54: j after resetting (nr. active dihedrals) = 46 -54: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg -54: Now calculating transitions... -54: Total number of transitions: 0 -54: Now printing out transitions and OPs... -54: Now printing out rotamer occupancies... -54: Now calculating Chi product trajectories... -54: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg -54: [ OK ] GmxChiTest.gmxchiWorksWithAll (1928 ms) -54: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN -54: Analyzing from residue 2 to residue 6 -54: 5 residues with dihedrals found -54: 23 dihedrals found -54: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. -54: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 -54: j after resetting (nr. active dihedrals) = 23 -54: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg -54: Now calculating transitions... -54: Total number of transitions: 0 -54: Now printing out transitions and OPs... -54: Now printing out rotamer occupancies... -54: Now calculating Chi product trajectories... -54: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg -54: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (1377 ms) -54: [----------] 2 tests from GmxChiTest (3384 ms total) -54: -54: [----------] 10 tests from MindistTest -54: [ RUN ] MindistTest.mindistWorksWithSingleAtoms -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 0: 'atom1' -54: Selected 1: 'atom2' -54: [ OK ] MindistTest.mindistWorksWithSingleAtoms (214 ms) -54: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 2: 'atom3' -54: Selected 3: 'atoms12' -54: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (82 ms) -54: [ RUN ] MindistTest.mindistDoesNotPickUpContacts -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 0: 'atom1' -54: Selected 1: 'atom2' -54: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) -54: [ RUN ] MindistTest.mindistPicksUpContacts -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 0: 'atom1' -54: Selected 1: 'atom2' -54: [ OK ] MindistTest.mindistPicksUpContacts (106 ms) -54: [ RUN ] MindistTest.ngWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 0: 'atom1' -54: Selected 1: 'atom2' -54: Selected 2: 'atom3' -54: [ OK ] MindistTest.ngWorks (1 ms) -54: [ RUN ] MindistTest.groupWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 3: 'atoms12' -54: Selected 2: 'atom3' -54: [ OK ] MindistTest.groupWorks (318 ms) -54: [ RUN ] MindistTest.maxDistWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 2: 'atom3' -54: Selected 3: 'atoms12' -54: [ OK ] MindistTest.maxDistWorks (0 ms) -54: [ RUN ] MindistTest.noPbcWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 0: 'atom1' -54: Selected 1: 'atom2' -54: [ OK ] MindistTest.noPbcWorks (0 ms) -54: [ RUN ] MindistTest.resPerTimeWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 3: 'atoms12' -54: Selected 2: 'atom3' -54: [ OK ] MindistTest.resPerTimeWorks (316 ms) -54: [ RUN ] MindistTest.matrixWorks -54: Group 0 ( atom1) has 1 elements -54: Group 1 ( atom2) has 1 elements -54: Group 2 ( atom3) has 1 elements -54: Group 3 ( atoms12) has 2 elements -54: Group 4 ( atoms23) has 2 elements -54: Group 5 ( atoms123) has 3 elements -54: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. -54: Reading frame 0 time 0.000 Last frame 0 time 0.000 -54: Selected 5: 'atoms123' -54: Special case: making distance matrix between all atoms in group atoms123 -54: [ OK ] MindistTest.matrixWorks (0 ms) -54: [----------] 10 tests from MindistTest (1043 ms total) -54: -54: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: trr version: GMX_trn_file (single precision) -54: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -54: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -54: Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) -54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 -54: Group 0 ( System) has 6 elements -54: Group 1 ( Water) has 6 elements -54: Group 2 ( SOL) has 6 elements -54: Select a group: Reading frame 0 time 0.000 -54: WARNING: If there are molecules in the input trajectory file -54: that are broken across periodic boundaries, they -54: cannot be made whole (or treated as whole) without -54: you providing a run input file. -54: -54: Reading frame 1 time 1.000 Last frame 1 time 1.000 -54: -54: WARNING: Masses and atomic (Van der Waals) radii will be guessed -54: based on residue and atom names, since they could not be -54: definitively assigned from the information in your input -54: files. These guessed numbers might deviate from the mass -54: and radius of the atom type. Please check the output -54: files if necessary. Note, that this functionality may -54: be removed in a future GROMACS version. Please, consider -54: using another file format for your input. -54: -54: Selected 0: 'System' -54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) -54: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (15 ms total) -54: -54: [----------] Global test environment tear-down -54: [==========] 31 tests from 4 test suites ran. (4443 ms total) -54: [ PASSED ] 31 tests. -54/96 Test #54: GmxAnaTest ................................... Passed 4.75 sec -test 55 - Start 55: GmxPreprocessTests - -55: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" -55: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests -55: Test timeout computed to be: 1920 -55: [==========] Running 260 tests from 16 test suites. -55: [----------] Global test environment set-up. -55: [----------] 1 test from ConvertInteractionsTest -55: [ RUN ] ConvertInteractionsTest.DoingNothingWorks -55: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) -55: [----------] 1 test from ConvertInteractionsTest (0 ms total) -55: -55: [----------] 4 tests from GenconfTest -55: [ RUN ] GenconfTest.nbox_Works -55: [ OK ] GenconfTest.nbox_Works (0 ms) -55: [ RUN ] GenconfTest.nbox_norenumber_Works -55: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) -55: [ RUN ] GenconfTest.nbox_dist_Works -55: [ OK ] GenconfTest.nbox_dist_Works (0 ms) -55: [ RUN ] GenconfTest.nbox_rot_Works -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: center of geometry: 1.733667, 1.477000, 0.905167 -55: [ OK ] GenconfTest.nbox_rot_Works (0 ms) -55: [----------] 4 tests from GenconfTest (2 ms total) -55: -55: [----------] 2 tests from GenionTest -55: [ RUN ] GenionTest.HighConcentrationIonPlacement -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -55: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -55: buffer. The cluster pair list does have a buffering effect, but choosing -55: a larger rlist might be necessary for good energy conservation. -55: -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -55: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -55: < 0 -55: -55: -55: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: Generating 1-4 interactions: fudge = 0.5 -55: Number of degrees of freedom in T-Coupling group rest is 1308.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: -55: You are using a plain Coulomb cut-off, which might produce artifacts. -55: You might want to consider using PME electrostatics. -55: -55: -55: -55: There were 4 NOTEs -55: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -55: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -55: Group 0 ( System) has 653 elements -55: Group 1 ( Water) has 648 elements -55: Group 2 ( SOL) has 648 elements -55: Group 3 ( non-Water) has 5 elements -55: Group 4 ( Other) has 5 elements -55: Group 5 ( METH) has 5 elements -55: Select a group: Number of (3-atomic) solvent molecules: 216 -55: Using random seed 1997. -55: Replacing solvent molecule 56 (atom 168) with NA -55: Replacing solvent molecule 120 (atom 360) with NA -55: Replacing solvent molecule 182 (atom 546) with NA -55: Replacing solvent molecule 71 (atom 213) with NA -55: Replacing solvent molecule 189 (atom 567) with CL -55: Replacing solvent molecule 54 (atom 162) with CL -55: Replacing solvent molecule 155 (atom 465) with CL -55: Replacing solvent molecule 99 (atom 297) with CL -55: -55: Setting the LD random seed to 1878905855 -55: -55: Generated 331705 of the 331705 non-bonded parameter combinations -55: -55: Generated 331705 of the 331705 1-4 parameter combinations -55: -55: Excluding 2 bonded neighbours molecule type 'SOL' -55: -55: Excluding 3 bonded neighbours molecule type 'methane' -55: -55: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -55: Analysing residue names: -55: There are: 216 Water residues -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: This run will generate roughly 0 Mb of data -55: Will try to add 4 NA ions and 4 CL ions. -55: Select a continuous group of solvent molecules -55: Selected 1: 'Water' -55: [ OK ] GenionTest.HighConcentrationIonPlacement (237 ms) -55: [ RUN ] GenionTest.NoIonPlacement -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -55: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet -55: buffer. The cluster pair list does have a buffering effect, but choosing -55: a larger rlist might be necessary for good energy conservation. -55: -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -55: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -55: < 0 -55: -55: -55: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: Generating 1-4 interactions: fudge = 0.5 -55: Number of degrees of freedom in T-Coupling group rest is 1308.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: -55: You are using a plain Coulomb cut-off, which might produce artifacts. -55: You might want to consider using PME electrostatics. -55: -55: -55: -55: There were 4 NOTEs -55: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -55: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -55: No ions to add, will just copy input configuration. -55: Setting the LD random seed to -33622147 -55: -55: Generated 331705 of the 331705 non-bonded parameter combinations -55: -55: Generated 331705 of the 331705 1-4 parameter combinations -55: -55: Excluding 2 bonded neighbours molecule type 'SOL' -55: -55: Excluding 3 bonded neighbours molecule type 'methane' -55: -55: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216_with_methane.gro' -55: Analysing residue names: -55: There are: 216 Water residues -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] GenionTest.NoIonPlacement (726 ms) -55: [----------] 2 tests from GenionTest (963 ms total) -55: -55: [----------] 1 test from GenRestrTest -55: [ RUN ] GenRestrTest.SimpleRestraintsGenerated -55: -55: Reading structure file -55: Group 0 ( System) has 156 elements -55: Group 1 ( Protein) has 156 elements -55: Group 2 ( Protein-H) has 75 elements -55: Group 3 ( C-alpha) has 10 elements -55: Group 4 ( Backbone) has 30 elements -55: Group 5 ( MainChain) has 40 elements -55: Group 6 ( MainChain+Cb) has 49 elements -55: Group 7 ( MainChain+H) has 52 elements -55: Group 8 ( SideChain) has 104 elements -55: Group 9 ( SideChain-H) has 35 elements -55: Select a group: Select group to position restrain -55: Selected 3: 'C-alpha' -55: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) -55: [----------] 1 test from GenRestrTest (1 ms total) -55: -55: [----------] 9 tests from PreprocessingAtomTypesTest -55: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate -55: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid -55: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks -55: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks -55: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry -55: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound -55: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound -55: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber -55: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) -55: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber -55: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) -55: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) -55: -55: [----------] 10 tests from PreprocessingBondAtomTypeTest -55: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate -55: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid -55: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks -55: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks -55: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry -55: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType -55: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound -55: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound -55: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber -55: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) -55: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber -55: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) -55: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) -55: -55: [----------] 3 tests from GromppDirectiveTest -55: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives.top, line 59]: -55: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 9.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -55: Setting the LD random seed to -168255651 -55: -55: Generated 10 of the 10 non-bonded parameter combinations -55: -55: Generated 10 of the 10 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -276832770 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (270 ms) -55: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives.top, line 59]: -55: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have -55: coefficients that do not sum to zero. This does not affect the simulation -55: and can be ignored, unless you are comparing potential energy values with -55: other force field ports and/or MD software. -55: First such dihedral in molecule A, involving atoms 0 2 1 3 -55: -55: -55: NOTE 2 [file directives.top, line 59]: -55: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 9.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 3 NOTEs -55: Setting the LD random seed to -1308623445 -55: -55: Generated 10 of the 10 non-bonded parameter combinations -55: -55: Generated 10 of the 10 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -84475925 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (130 ms) -55: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy -55: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (0 ms) -55: [----------] 3 tests from GromppDirectiveTest (401 ms total) -55: -55: [----------] 6 tests from InsertMoleculesTest -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration -55: Reading solute configuration -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Try 1 success (now 8 atoms)! -55: -55: Added 1 molecules (out of 1 requested) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro -55: -55: Output configuration contains 8 atoms in 4 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Try 1 success (now 2 atoms)! -55: Try 2 success (now 4 atoms)! -55: Try 3 success (now 6 atoms)! -55: Try 4 success (now 8 atoms)! -55: Try 5 success (now 10 atoms)! -55: -55: Added 5 molecules (out of 5 requested) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro -55: -55: Output configuration contains 10 atoms in 10 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (150 ms) -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Try 1 success (now 2 atoms)! -55: Try 2 success (now 4 atoms)! -55: Try 3 success (now 6 atoms)! -55: Try 4 success (now 8 atoms)! -55: Try 5 success (now 10 atoms)! -55: -55: Added 5 molecules (out of 5 requested) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro -55: -55: Output configuration contains 10 atoms in 10 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (73 ms) -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox -55: Reading solute configuration -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Try 1 success (now 8 atoms)! -55: Try 2 success (now 10 atoms)! -55: -55: Added 2 molecules (out of 2 requested) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro -55: -55: Output configuration contains 10 atoms in 4 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement -55: Reading solute configuration -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Try 1 success (now 650 atoms)! -55: Try 2 success (now 652 atoms)! -55: Try 3 success (now 654 atoms)! -55: Try 4 success (now 656 atoms)! -55: -55: Added 4 molecules (out of 4 requested) -55: Replaced 8 residues (24 atoms) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro -55: -55: Output configuration contains 632 atoms in 212 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (113 ms) -55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Using random seed 1997 -55: Read 4 positions from file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat -55: -55: Try 1 success (now 2 atoms)! -55: Try 2 success (now 4 atoms)! -55: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) -55: Try 13 success (now 6 atoms)! -55: -55: Added 3 molecules (out of 4 requested) -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro -55: -55: Output configuration contains 6 atoms in 3 residues -55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (43 ms) -55: [----------] 6 tests from InsertMoleculesTest (382 ms total) -55: -55: [----------] 3 tests from MassRepartitioning -55: [ RUN ] MassRepartitioning.ValidCaseWorks -55: The smallest mass in the system is 2, setting the minimum mass to 6 -55: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) -55: [ RUN ] MassRepartitioning.UnboundGivesWarning -55: -55: WARNING 1 [file unknown]: -55: The are 1 atoms that have a mass below the mass repartitioning limit but -55: are not bound. These masses cannot be repartitioned. -55: -55: The smallest mass in the system is 2, setting the minimum mass to 6 -55: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) -55: [ RUN ] MassRepartitioning.LightPartnerGivesError -55: -55: ERROR 1 [file unknown]: -55: Light atoms are bound to at least one atom that has a too low mass for -55: repartitioning -55: -55: The smallest mass in the system is 2, setting the minimum mass to 6 -55: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) -55: [----------] 3 tests from MassRepartitioning (0 ms total) -55: -55: [----------] 35 tests from GetIrTest -55: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines -55: Ignoring obsolete mdp entry 'title' -55: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (7 ms) -55: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals -55: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) -55: [ RUN ] GetIrTest.AcceptsKeyWithoutValue -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsKeyWithoutValue (99 ms) -55: [ RUN ] GetIrTest.RejectsValueWithoutKey -55: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) -55: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue -55: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) -55: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) -55: [ RUN ] GetIrTest.AcceptsEmptyLines -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsEmptyLines (103 ms) -55: [ RUN ] GetIrTest.MtsCheckNstcalcenergy -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -55: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) -55: [ RUN ] GetIrTest.MtsCheckNstenergy -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -55: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -55: Setting nstcalcenergy (100) equal to nstenergy (5) -55: -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) -55: [ RUN ] GetIrTest.MtsCheckNstpcouple -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -55: Pressure coupling incorrect number of values (I need exactly 1) -55: -55: -55: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: -55: Pressure coupling incorrect number of values (I need exactly 1) -55: -55: -55: ERROR 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -55: With multiple time stepping, nstpcouple should be a multiple of -55: mts-factor -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: -55: ERROR 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -55: The Berendsen barostat does not generate any strictly correct ensemble, -55: and should not be used for new production simulations (in our opinion). -55: We recommend using the C-rescale barostat instead. -55: -55: -55: ERROR 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: -55: compressibility must be > 0 when using pressure coupling Berendsen -55: -55: -55: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) -55: [ RUN ] GetIrTest.MtsCheckNstdhdl -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -55: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -55: Setting nstcalcenergy (100) equal to nstdhdl (5) -55: -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: -55: ERROR 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: -55: Lambda state must be set, either with init-lambda-state or with -55: init-lambda -55: -55: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) -55: [ RUN ] GetIrTest.MtsCheckSDNotSupported -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -55: Multiple time stepping is only supported with integrator md -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) -55: [ RUN ] GetIrTest.AcceptsElectricField -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsElectricField (1 ms) -55: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (148 ms) -55: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (74 ms) -55: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys -55: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) -55: [ RUN ] GetIrTest.AcceptsImplicitSolventNo -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsImplicitSolventNo (70 ms) -55: [ RUN ] GetIrTest.RejectsImplicitSolventYes -55: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) -55: [ RUN ] GetIrTest.AcceptsMimic -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsMimic (1 ms) -55: [ RUN ] GetIrTest.AcceptsTransformationCoord -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: -55: pull-coord2 has a non-zero force constant and is also referenced in -55: pull-coord1-expression. Make sure that this is intended. In most use -55: cases, the pull coordinates referenced by a transformation coordinate -55: should have their force constant set to zero. -55: -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.AcceptsTransformationCoord (151 ms) -55: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: -55: pull-coord1 cannot have type 'constraint' and geometry 'transformation' -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) -55: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: -55: pull-coord2 can not use pull-coord1 in the transformation since this is a -55: constraint -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) -55: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: -55: pull-coord1-dx cannot be set to zero for pull coordinate of geometry -55: 'transformation' -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (146 ms) -55: [ RUN ] GetIrTest.MissingTransformationCoordExpression -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: -55: pull-coord1-expression not set for pull coordinate of geometry -55: 'transformation' -55: -55: -55: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: -55: For a correct single-point energy evaluation with nsteps = 0, use -55: continuation = yes to avoid constraining the input coordinates. -55: -55: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep -55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta -55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep -55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta -55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: -55: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, -55: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of -55: in total 100001 steps. This is not compatible with using soft-core -55: potentials. -55: -55: -55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: -55: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -55: won't change anymore after step 100000 until the end of the simulation -55: after 100001 steps. -55: -55: -55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: -55: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components -55: won't change anymore after step 100000 until the end of the simulation -55: after 100001 steps. -55: -55: -55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: -55: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda -55: components won't change anymore after step 100000 until the end of the -55: simulation after 100001 steps. -55: -55: -55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta -55: -55: ERROR 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: -55: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda -55: components won't change anymore after step 100000 until the end of the -55: simulation after 100001 steps. -55: -55: -55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep -55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) -55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta -55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) -55: [----------] 35 tests from GetIrTest (834 ms total) -55: -55: [----------] 6 tests from SolvateTest -55: [ RUN ] SolvateTest.cs_box_Works -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 1x1x1 boxes -55: Solvent box contains 270 atoms in 90 residues -55: Removed 129 solvent atoms due to solvent-solvent overlap -55: Sorting configuration -55: Found 1 molecule type: -55: SOL ( 3 atoms): 47 residues -55: Generated solvent containing 141 atoms in 47 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro -55: -55: Output configuration contains 141 atoms in 47 residues -55: Volume : 1.331 (nm^3) -55: Density : 1056.36 (g/l) -55: Number of solvent molecules: 47 -55: -55: [ OK ] SolvateTest.cs_box_Works (3 ms) -55: [ RUN ] SolvateTest.cs_cp_Works -55: Reading solute configuration -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 2x2x2 boxes -55: Solvent box contains 3660 atoms in 1220 residues -55: Removed 987 solvent atoms due to solvent-solvent overlap -55: Removed 15 solvent atoms due to solute-solvent overlap -55: Sorting configuration -55: Found 1 molecule type: -55: SOL ( 3 atoms): 886 residues -55: Generated solvent containing 2658 atoms in 886 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro -55: -55: Output configuration contains 2664 atoms in 888 residues -55: Volume : 27.2709 (nm^3) -55: Density : 974.777 (g/l) -55: Number of solvent molecules: 886 -55: -55: [ OK ] SolvateTest.cs_cp_Works (13 ms) -55: [ RUN ] SolvateTest.cs_cp_p_Works -55: Reading solute configuration -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 2x2x2 boxes -55: Solvent box contains 3660 atoms in 1220 residues -55: Removed 987 solvent atoms due to solvent-solvent overlap -55: Removed 15 solvent atoms due to solute-solvent overlap -55: Sorting configuration -55: Found 1 molecule type: -55: SOL ( 3 atoms): 886 residues -55: Generated solvent containing 2658 atoms in 886 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro -55: -55: Output configuration contains 2664 atoms in 888 residues -55: Volume : 27.2709 (nm^3) -55: Density : 974.777 (g/l) -55: Number of solvent molecules: 886 -55: -55: Processing topology -55: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) -55: [ OK ] SolvateTest.cs_cp_p_Works (651 ms) -55: [ RUN ] SolvateTest.shell_Works -55: Reading solute configuration -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 2x2x2 boxes -55: Solvent box contains 3660 atoms in 1220 residues -55: Removed 987 solvent atoms due to solvent-solvent overlap -55: Removed 1902 solvent atoms more than 1.000000 nm from solute. -55: Removed 15 solvent atoms due to solute-solvent overlap -55: Sorting configuration -55: Found 1 molecule type: -55: SOL ( 3 atoms): 252 residues -55: Generated solvent containing 756 atoms in 252 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro -55: -55: Output configuration contains 762 atoms in 254 residues -55: Volume : 27.2709 (nm^3) -55: Density : 279.3 (g/l) -55: Number of solvent molecules: 252 -55: -55: [ OK ] SolvateTest.shell_Works (38 ms) -55: [ RUN ] SolvateTest.update_Topology_Works -55: Reading solute configuration -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 3x3x3 boxes -55: Solvent box contains 14952 atoms in 4984 residues -55: Removed 2787 solvent atoms due to solvent-solvent overlap -55: Removed 30 solvent atoms due to solute-solvent overlap -55: Sorting configuration -55: Found 2 different molecule types: -55: HOH ( 3 atoms): 1876 residues -55: SOL ( 3 atoms): 2169 residues -55: Generated solvent containing 0 atoms in 0 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro -55: -55: Output configuration contains 12141 atoms in 4047 residues -55: Volume : 125 (nm^3) -55: Density : 968.963 (g/l) -55: Number of solvent molecules: 4045 -55: -55: Processing topology -55: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -55: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) -55: [ OK ] SolvateTest.update_Topology_Works (246 ms) -55: [ RUN ] SolvateTest.cs_pdb_big_box_Works -55: Reading solvent configuration -55: -55: Initialising inter-atomic distances... -55: -55: WARNING: Masses and atomic (Van der Waals) radii will be guessed -55: based on residue and atom names, since they could not be -55: definitively assigned from the information in your input -55: files. These guessed numbers might deviate from the mass -55: and radius of the atom type. Please check the output -55: files if necessary. Note, that this functionality may -55: be removed in a future GROMACS version. Please, consider -55: using another file format for your input. -55: -55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii -55: from the source below. This means the results may be different -55: compared to previous GROMACS versions. -55: -55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -55: A. Bondi -55: van der Waals Volumes and Radii -55: J. Phys. Chem. (1964) -55: DOI: 10.1021/j100785a001 -55: -------- -------- --- Thank You --- -------- -------- -55: -55: Generating solvent configuration -55: Will generate new solvent configuration of 2x2x2 boxes -55: Solvent box contains 1218 atoms in 406 residues -55: Removed 555 solvent atoms due to solvent-solvent overlap -55: Sorting configuration -55: Found 1 molecule type: -55: SOL ( 3 atoms): 221 residues -55: Generated solvent containing 663 atoms in 221 residues -55: Writing generated configuration to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro -55: -55: Output configuration contains 663 atoms in 221 residues -55: Volume : 8 (nm^3) -55: Density : 826.409 (g/l) -55: Number of solvent molecules: 221 -55: -55: [ OK ] SolvateTest.cs_pdb_big_box_Works (140 ms) -55: [----------] 6 tests from SolvateTest (1094 ms total) -55: -55: [----------] 1 test from TopDirTests -55: [ RUN ] TopDirTests.NamesArrayHasCorrectSize -55: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) -55: [----------] 1 test from TopDirTests (0 ms total) -55: -55: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N -55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) -55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped -55: Skipping interaction type that does not represent a interaction with parameters converted in grompp -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) -55: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (2 ms total) -55: -55: [----------] 45 tests from SinglePeptideFragments/EditconfTest -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (0 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 -55: -55: Select a group for output: -55: Group 0 ( two_residues) has 23 elements -55: There is one group in the index -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : 0.212 1.187 3.527 (nm) -55: new center : 4.028 2.819 3.723 (nm) -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.42 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.42 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.42 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: shift : -0.814 1.104 2.657 (nm) -55: new center : 3.002 2.736 2.852 (nm) -55: new box vectors : 6.004 5.472 5.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 187.40 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.28 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.28 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.28 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (2 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) -55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 -55: Note that major changes are planned in future for editconf, to improve usability and utility. -55: Read 252 atoms -55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons -55: No velocities found -55: system size : 2.004 1.472 1.704 (nm) -55: center : 3.816 1.632 0.195 (nm) -55: box vectors : 8.056 5.637 7.445 (nm) -55: box angles : 90.00 90.00 90.00 (degrees) -55: box volume : 338.10 (nm^3) -55: new center : 3.816 1.632 0.195 (nm) -55: new box vectors : 5.004 4.472 4.704 (nm) -55: new box angles : 90.00 90.00 90.00 (degrees) -55: new box volume : 105.27 (nm^3) -55: -55: WARNING: No boxtype specified - distance condition applied in each dimension. -55: If the molecule rotates the actual distance will be smaller. You might want -55: to use a cubic box instead, or why not try a dodecahedron today? -55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) -55: [----------] 45 tests from SinglePeptideFragments/EditconfTest (72 ms total) -55: -55: [----------] 16 tests from CorrectVelocity/MaxwellTest -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) -55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 -55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) -55: [----------] 16 tests from CorrectVelocity/MaxwellTest (9 ms total) -55: -55: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -67119370 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -171215906 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (78 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -17053347 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -8995141 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (337 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -671224857 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to 1207040894 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (11 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to 938978303 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -688391169 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (244 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -1351037953 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -1496041731 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (79 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -85591081 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to -46548496 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (66 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (0 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 -55: Ignoring obsolete mdp entry 'title' -55: Generating 1-4 interactions: fudge = 0.5 -55: -55: NOTE 1 [file directives-cmap.top, line 114]: -55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to -55: any other atom in the same moleculetype. Although technically this might -55: not cause issues in a simulation, this often means that the user forgot -55: to add a bond/potential/constraint or put multiple molecules in the same -55: moleculetype definition by mistake. Run with -v to get information for -55: each atom. -55: -55: Number of degrees of freedom in T-Coupling group rest is 12.00 -55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -55: -55: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: -55: NVE simulation: will use the initial temperature of 300.000 K for -55: determining the Verlet buffer size -55: -55: -55: There were 2 NOTEs -55: Setting the LD random seed to -25697283 -55: -55: Generated 3 of the 3 non-bonded parameter combinations -55: -55: Generated 3 of the 3 1-4 parameter combinations -55: -55: Excluding 0 bonded neighbours molecule type 'A' -55: -55: Setting gen_seed to 2128444923 -55: -55: Velocities were taken from a Maxwell distribution at 300 K -55: Analysing residue names: -55: There are: 1 Other residues -55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -55: -55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -55: -55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -55: -55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -55: -55: Note that mdrun will redetermine rlist based on the actual pair-list setup -55: -55: This run will generate roughly 0 Mb of data -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (54 ms) -55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 -55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (0 ms) -55: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (874 ms total) -55: -55: [----------] Global test environment tear-down -55: [==========] 260 tests from 16 test suites ran. (4640 ms total) -55: [ PASSED ] 220 tests. -55: [ SKIPPED ] 40 tests, listed below: -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl -55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl -55/96 Test #55: GmxPreprocessTests ........................... Passed 4.85 sec -test 56 - Start 56: Pdb2gmx1Test - -56: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" -56: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests -56: Test timeout computed to be: 1920 -56: [==========] Running 30 tests from 1 test suite. -56: [----------] Global test environment set-up. -56: [----------] 30 tests from Oplsaa/Pdb2gmxTest -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (55 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (90 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (185 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (126 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (364 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (160 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (248 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip3p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (121 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip4p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 0 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 0 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 0 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 0 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 0 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 25 donors and 23 acceptors were found. -56: There are 41 hydrogen bonds -56: Will use HISE for residue 8 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS3 HIS8 -56: SG9 NE251 -56: HIS8 NE251 1.055 -56: MET12 SD83 0.763 0.990 -56: Marked 124 virtual sites -56: Added 16 dummy masses -56: Added 26 new constraints -56: Before cleaning: 653 pairs -56: Before cleaning: 663 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 128 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (128 atoms, 16 residues) -56: -56: Identified residue ALA2 as a starting terminus. -56: -56: Identified residue SER17 as a ending terminus. -56: Start terminus ALA-2: NH3+ -56: End terminus SER-17: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 252 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 254, now 254 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 663 dihedrals, 51 impropers, 457 angles -56: 650 pairs, 254 bonds and 130 virtual sites -56: -56: Total mass 1846.112 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 30 donors and 22 acceptors were found. -56: There are 36 hydrogen bonds -56: Will use HISE for residue 29 -56: Will use HISE for residue 32 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS27 HIS29 -56: SG90 NE2111 -56: HIS29 NE2111 0.987 -56: HIS32 NE2135 1.590 1.155 -56: Marked 132 virtual sites -56: Added 10 dummy masses -56: Added 19 new constraints -56: Before cleaning: 748 pairs -56: Before cleaning: 778 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 149 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (149 atoms, 16 residues) -56: -56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue THR18 as a starting terminus. -56: -56: Identified residue PHE33 as a ending terminus. -56: Start terminus THR-18: NH3+ -56: End terminus PHE-33: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 281 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 290, now 290 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 778 dihedrals, 72 impropers, 516 angles -56: 736 pairs, 290 bonds and 133 virtual sites -56: -56: Total mass 2088.357 a.m.u. -56: -56: Total charge 1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 22 acceptors were found. -56: There are 26 hydrogen bonds -56: Will use HISE for residue 45 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS45 -56: NE295 -56: MET46 SD102 1.078 -56: Marked 123 virtual sites -56: Added 22 dummy masses -56: Added 35 new constraints -56: Before cleaning: 676 pairs -56: Before cleaning: 696 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 132 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (132 atoms, 16 residues) -56: -56: Identified residue ALA34 as a starting terminus. -56: -56: Identified residue ALA49 as a ending terminus. -56: Start terminus ALA-34: NH3+ -56: End terminus ALA-49: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 255 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 261, now 261 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 696 dihedrals, 56 impropers, 472 angles -56: 667 pairs, 261 bonds and 132 virtual sites -56: -56: Total mass 1861.128 a.m.u. -56: -56: Total charge -1.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 22 donors and 21 acceptors were found. -56: There are 30 hydrogen bonds -56: Will use HISE for residue 60 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: HIS60 -56: NE285 -56: CYS62 SG98 0.803 -56: Marked 111 virtual sites -56: Added 18 dummy masses -56: Added 31 new constraints -56: Before cleaning: 603 pairs -56: Before cleaning: 618 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -56: -56: chain #res #atoms -56: -56: 1 ' ' 16 117 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 (117 atoms, 16 residues) -56: -56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -56: -56: Identified residue LYS50 as a starting terminus. -56: -56: Identified residue PRO65 as a ending terminus. -56: Start terminus LYS-50: NH3+ -56: End terminus PRO-65: PRO-COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 16 residues with 228 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 232, now 232 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 618 dihedrals, 48 impropers, 419 angles -56: 597 pairs, 232 bonds and 116 virtual sites -56: -56: Total mass 1662.883 a.m.u. -56: -56: Total charge -0.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) -56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.r2b -56: All occupancies are one -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/atomtypes.atp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.rtp -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.hdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.n.tdb -56: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/oplsaa.ff/aminoacids.c.tdb -56: Analysing hydrogen-bonding network for automated assignment of histidine -56: protonation. 89 donors and 98 acceptors were found. -56: There are 129 hydrogen bonds -56: Will use HISE for residue 31 -56: Will use HISE for residue 51 -56: 9 out of 9 lines of specbond.dat converted successfully -56: Special Atom Distance matrix: -56: CYS25 HIS31 HIS51 -56: SG14 NE264 NE2226 -56: HIS31 NE264 1.921 -56: HIS51 NE2226 1.498 2.650 -56: CYS80 SG477 0.207 1.984 1.570 -56: Linking CYS-25 SG-14 and CYS-80 SG-477... -56: Marked 447 virtual sites -56: Added 58 dummy masses -56: Added 101 new constraints -56: Before cleaning: 2499 pairs -56: Before cleaning: 2524 dihedrals -56: Using the Oplsaa force field in directory oplsaa.ff -56: -56: going to rename oplsaa.ff/aminoacids.r2b -56: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -56: -56: Analyzing pdb file -56: Splitting chemical chains based on TER records or chain id changing. -56: -56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -56: -56: chain #res #atoms -56: -56: 1 'A' 58 488 -56: -56: All occupancies are one -56: -56: Reading residue database... (Oplsaa) -56: -56: Processing chain 1 'A' (488 atoms, 58 residues) -56: -56: Identified residue ASN24 as a starting terminus. -56: -56: Identified residue ARG81 as a ending terminus. -56: Start terminus ASN-24: NH3+ -56: End terminus ARG-81: COO- -56: -56: Checking for duplicate atoms.... -56: -56: Generating any missing hydrogen atoms and/or adding termini. -56: -56: Now there are 58 residues with 936 atoms -56: -56: Making bonds... -56: -56: Number of bonds was 951, now 951 -56: -56: Generating angles, dihedrals and pairs... -56: -56: Making cmap torsions... -56: -56: There are 2524 dihedrals, 208 impropers, 1704 angles -56: 2469 pairs, 951 bonds and 462 virtual sites -56: -56: Total mass 6908.578 a.m.u. -56: -56: Total charge -6.000 e -56: -56: Writing topology -56: -56: Writing coordinate file... -56: -56: --------- PLEASE NOTE ------------ -56: -56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -56: -56: The Oplsaa force field and the tip5p water model are used. -56: -56: --------- ETON ESAELP ------------ -56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) -56: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1983 ms total) -56: -56: [----------] Global test environment tear-down -56: [==========] 30 tests from 1 test suite ran. (1983 ms total) -56: [ PASSED ] 30 tests. -56/96 Test #56: Pdb2gmx1Test ................................. Passed 2.20 sec -test 57 - Start 57: Pdb2gmx2Test - -57: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" -57: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests -57: Test timeout computed to be: 1920 -57: [==========] Running 40 tests from 2 test suites. -57: [----------] Global test environment set-up. -57: [----------] 20 tests from G43a1/Pdb2gmxTest -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 305 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 165 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 172, now 167 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 77 impropers, 241 angles -57: 267 pairs, 167 bonds and 0 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 429 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 202 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 216, now 211 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 134 impropers, 316 angles -57: 273 pairs, 211 bonds and 0 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 349 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 168 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 179, now 174 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 102 impropers, 260 angles -57: 242 pairs, 174 bonds and 0 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 299 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 150 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 159, now 154 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 80 impropers, 227 angles -57: 232 pairs, 154 bonds and 0 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1256 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 635 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 655, now 650 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 350 impropers, 955 angles -57: 972 pairs, 650 bonds and 0 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 37 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 305 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 165 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 172, now 167 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 77 impropers, 241 angles -57: 267 pairs, 167 bonds and 37 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 53 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 429 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 202 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 216, now 211 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 134 impropers, 316 angles -57: 273 pairs, 211 bonds and 51 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 36 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 349 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 168 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 179, now 174 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 102 impropers, 260 angles -57: 242 pairs, 174 bonds and 36 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 33 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 299 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 150 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 159, now 154 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 80 impropers, 227 angles -57: 232 pairs, 154 bonds and 31 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 146 virtual sites -57: Added 10 dummy masses -57: Added 29 new constraints -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1256 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 635 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 655, now 650 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 350 impropers, 955 angles -57: 972 pairs, 650 bonds and 137 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos43a1 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 305 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 165 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 172, now 167 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 77 impropers, 241 angles -57: 267 pairs, 167 bonds and 0 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 429 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 202 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 216, now 211 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 134 impropers, 316 angles -57: 273 pairs, 211 bonds and 0 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 349 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 168 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 179, now 174 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 102 impropers, 260 angles -57: 242 pairs, 174 bonds and 0 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 299 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 150 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 159, now 154 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 80 impropers, 227 angles -57: 232 pairs, 154 bonds and 0 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1256 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 635 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 655, now 650 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 350 impropers, 955 angles -57: 972 pairs, 650 bonds and 0 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 37 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 305 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 165 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 172, now 167 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 77 impropers, 241 angles -57: 267 pairs, 167 bonds and 37 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 53 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 429 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 202 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 216, now 211 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 134 impropers, 316 angles -57: 273 pairs, 211 bonds and 51 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 36 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 349 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 168 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 179, now 174 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 102 impropers, 260 angles -57: 242 pairs, 174 bonds and 36 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 33 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 299 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 150 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 159, now 154 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 80 impropers, 227 angles -57: 232 pairs, 154 bonds and 31 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge 0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.rtp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos43a1.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 146 virtual sites -57: Added 10 dummy masses -57: Added 29 new constraints -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1256 dihedrals -57: Using the Gromos43a1 force field in directory gromos43a1.ff -57: -57: going to rename gromos43a1.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos43a1) -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 635 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 655, now 650 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 350 impropers, 955 angles -57: 972 pairs, 650 bonds and 137 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos43a1 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (60 ms) -57: [----------] 20 tests from G43a1/Pdb2gmxTest (544 ms total) -57: -57: [----------] 20 tests from G53a6/Pdb2gmxTest -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 312 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 167 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 174, now 169 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 79 impropers, 245 angles -57: 267 pairs, 169 bonds and 0 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 443 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 206 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 220, now 215 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 138 impropers, 324 angles -57: 273 pairs, 215 bonds and 0 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (29 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 356 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 170 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 181, now 176 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 104 impropers, 264 angles -57: 242 pairs, 176 bonds and 0 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (27 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 306 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 152 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 161, now 156 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 82 impropers, 231 angles -57: 232 pairs, 156 bonds and 0 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1270 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 639 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 659, now 654 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 354 impropers, 963 angles -57: 972 pairs, 654 bonds and 0 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 39 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 312 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 167 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 174, now 169 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 79 impropers, 245 angles -57: 267 pairs, 169 bonds and 39 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 57 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 443 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 206 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 220, now 215 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 138 impropers, 324 angles -57: 273 pairs, 215 bonds and 55 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 38 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 356 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 170 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 181, now 176 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 104 impropers, 264 angles -57: 242 pairs, 176 bonds and 38 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 35 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 306 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 152 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 161, now 156 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 82 impropers, 231 angles -57: 232 pairs, 156 bonds and 33 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 150 virtual sites -57: Added 10 dummy masses -57: Added 29 new constraints -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1270 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 639 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 659, now 654 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 354 impropers, 963 angles -57: 972 pairs, 654 bonds and 141 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos53a6 force field and the spc water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 312 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 167 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 174, now 169 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 79 impropers, 245 angles -57: 267 pairs, 169 bonds and 0 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 443 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 206 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 220, now 215 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 138 impropers, 324 angles -57: 273 pairs, 215 bonds and 0 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 356 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 170 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 181, now 176 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 104 impropers, 264 angles -57: 242 pairs, 176 bonds and 0 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 306 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 152 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 161, now 156 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 82 impropers, 231 angles -57: 232 pairs, 156 bonds and 0 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1270 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 639 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 659, now 654 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 354 impropers, 963 angles -57: 972 pairs, 654 bonds and 0 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 25 donors and 23 acceptors were found. -57: There are 41 hydrogen bonds -57: Will use HISE for residue 8 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS3 HIS8 -57: SG9 NE251 -57: HIS8 NE251 1.055 -57: MET12 SD83 0.763 0.990 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 39 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 267 pairs -57: Before cleaning: 312 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 128 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (128 atoms, 16 residues) -57: -57: Identified residue ALA2 as a starting terminus. -57: -57: Identified residue SER17 as a ending terminus. -57: Start terminus ALA-2: NH3+ -57: End terminus SER-17: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 167 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 174, now 169 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 90 dihedrals, 79 impropers, 245 angles -57: 267 pairs, 169 bonds and 39 virtual sites -57: -57: Total mass 1846.116 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 30 donors and 22 acceptors were found. -57: There are 36 hydrogen bonds -57: Will use HISE for residue 29 -57: Will use HISE for residue 32 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS27 HIS29 -57: SG90 NE2111 -57: HIS29 NE2111 0.987 -57: HIS32 NE2135 1.590 1.155 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 57 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 273 pairs -57: Before cleaning: 443 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 149 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (149 atoms, 16 residues) -57: -57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue THR18 as a starting terminus. -57: -57: Identified residue PHE33 as a ending terminus. -57: Start terminus THR-18: NH3+ -57: End terminus PHE-33: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 206 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 220, now 215 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 93 dihedrals, 138 impropers, 324 angles -57: 273 pairs, 215 bonds and 55 virtual sites -57: -57: Total mass 2088.361 a.m.u. -57: -57: Total charge 1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 22 acceptors were found. -57: There are 26 hydrogen bonds -57: Will use HISE for residue 45 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS45 -57: NE295 -57: MET46 SD102 1.078 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 38 virtual sites -57: Added 4 dummy masses -57: Added 8 new constraints -57: -57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 242 pairs -57: Before cleaning: 356 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 132 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (132 atoms, 16 residues) -57: -57: Identified residue ALA34 as a starting terminus. -57: -57: Identified residue ALA49 as a ending terminus. -57: Start terminus ALA-34: NH3+ -57: End terminus ALA-49: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 170 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 181, now 176 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 81 dihedrals, 104 impropers, 264 angles -57: 242 pairs, 176 bonds and 38 virtual sites -57: -57: Total mass 1861.132 a.m.u. -57: -57: Total charge -1.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 22 donors and 21 acceptors were found. -57: There are 30 hydrogen bonds -57: Will use HISE for residue 60 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: HIS60 -57: NE285 -57: CYS62 SG98 0.803 -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 35 virtual sites -57: Added 4 dummy masses -57: Added 10 new constraints -57: -57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 232 pairs -57: Before cleaning: 306 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -57: -57: chain #res #atoms -57: -57: 1 ' ' 16 117 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 (117 atoms, 16 residues) -57: -57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -57: -57: Identified residue LYS50 as a starting terminus. -57: -57: Identified residue PRO65 as a ending terminus. -57: Start terminus LYS-50: NH3+ -57: End terminus PRO-65: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 16 residues with 152 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 161, now 156 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 78 dihedrals, 82 impropers, 231 angles -57: 232 pairs, 156 bonds and 33 virtual sites -57: -57: Total mass 1662.887 a.m.u. -57: -57: Total charge -0.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) -57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.r2b -57: All occupancies are one -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/atomtypes.atp -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.rtp -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.hdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.n.tdb -57: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/gromos53a6.ff/aminoacids.c.tdb -57: Analysing hydrogen-bonding network for automated assignment of histidine -57: protonation. 89 donors and 98 acceptors were found. -57: There are 129 hydrogen bonds -57: Will use HISE for residue 31 -57: Will use HISE for residue 51 -57: 9 out of 9 lines of specbond.dat converted successfully -57: Special Atom Distance matrix: -57: CYS25 HIS31 HIS51 -57: SG14 NE264 NE2226 -57: HIS31 NE264 1.921 -57: HIS51 NE2226 1.498 2.650 -57: CYS80 SG477 0.207 1.984 1.570 -57: Linking CYS-25 SG-14 and CYS-80 SG-477... -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: -57: WARNING: Duplicate line found in or between hackblock and rtp entries -57: -57: Marked 150 virtual sites -57: Added 10 dummy masses -57: Added 29 new constraints -57: -57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom H used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: -57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped -57: to an entry in the topology database, but the atom O used in -57: an interaction of type angle in that entry is not found in the -57: input file. Perhaps your atom and/or residue naming needs to be -57: fixed. -57: -57: -57: Before cleaning: 972 pairs -57: Before cleaning: 1270 dihedrals -57: Using the Gromos53a6 force field in directory gromos53a6.ff -57: -57: going to rename gromos53a6.ff/aminoacids.r2b -57: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -57: -57: Analyzing pdb file -57: Splitting chemical chains based on TER records or chain id changing. -57: -57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -57: -57: chain #res #atoms -57: -57: 1 'A' 58 488 -57: -57: All occupancies are one -57: -57: Reading residue database... (Gromos53a6) -57: -57: Using default: not generating all possible dihedrals -57: -57: Using default: excluding 3 bonded neighbors -57: -57: Using default: generating 1,4 H--H interactions -57: -57: Using default: removing proper dihedrals found on the same bond as a proper dihedral -57: -57: Processing chain 1 'A' (488 atoms, 58 residues) -57: -57: Identified residue ASN24 as a starting terminus. -57: -57: Identified residue ARG81 as a ending terminus. -57: Start terminus ASN-24: NH3+ -57: End terminus ARG-81: COO- -57: -57: Checking for duplicate atoms.... -57: -57: Generating any missing hydrogen atoms and/or adding termini. -57: -57: Now there are 58 residues with 639 atoms -57: -57: Making bonds... -57: -57: Number of bonds was 659, now 654 -57: -57: Generating angles, dihedrals and pairs... -57: -57: Making cmap torsions... -57: -57: There are 321 dihedrals, 354 impropers, 963 angles -57: 972 pairs, 654 bonds and 141 virtual sites -57: -57: Total mass 6908.582 a.m.u. -57: -57: Total charge -6.000 e -57: -57: Writing topology -57: -57: Writing coordinate file... -57: -57: --------- PLEASE NOTE ------------ -57: -57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -57: -57: The Gromos53a6 force field and the spce water model are used. -57: -57: --------- ETON ESAELP ------------ -57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) -57: [----------] 20 tests from G53a6/Pdb2gmxTest (579 ms total) -57: -57: [----------] Global test environment tear-down -57: [==========] 40 tests from 2 test suites ran. (1123 ms total) -57: [ PASSED ] 40 tests. -57/96 Test #57: Pdb2gmx2Test ................................. Passed 1.32 sec -test 58 - Start 58: Pdb2gmx3Test - -58: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" -58: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/gmxpreprocess/tests -58: Test timeout computed to be: 1920 -58: [==========] Running 39 tests from 6 test suites. -58: [----------] Global test environment set-up. -58: [----------] 10 tests from Amber/Pdb2gmxTest -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Before cleaning: 653 pairs -58: Before cleaning: 691 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 128 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (128 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 252 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 255, now 254 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 691 dihedrals, 51 impropers, 457 angles -58: 650 pairs, 254 bonds and 0 virtual sites -58: -58: Total mass 1846.132 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 30 donors and 22 acceptors were found. -58: There are 36 hydrogen bonds -58: Will use HISE for residue 29 -58: Will use HISE for residue 32 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS27 HIS29 -58: SG90 NE2111 -58: HIS29 NE2111 0.987 -58: HIS32 NE2135 1.590 1.155 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Before cleaning: 748 pairs -58: Before cleaning: 788 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 149 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (149 atoms, 16 residues) -58: -58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue PHE33 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 281 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 291, now 290 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 788 dihedrals, 72 impropers, 516 angles -58: 736 pairs, 290 bonds and 0 virtual sites -58: -58: Total mass 2088.366 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 22 acceptors were found. -58: There are 26 hydrogen bonds -58: Will use HISE for residue 45 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS45 -58: NE295 -58: MET46 SD102 1.078 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Before cleaning: 676 pairs -58: Before cleaning: 727 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 132 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (132 atoms, 16 residues) -58: -58: Identified residue ALA34 as a starting terminus. -58: -58: Identified residue ALA49 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 255 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 262, now 261 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 727 dihedrals, 56 impropers, 472 angles -58: 667 pairs, 261 bonds and 0 virtual sites -58: -58: Total mass 1861.124 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 21 acceptors were found. -58: There are 30 hydrogen bonds -58: Will use HISE for residue 60 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS60 -58: NE285 -58: CYS62 SG98 0.803 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Before cleaning: 603 pairs -58: Before cleaning: 634 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 117 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (117 atoms, 16 residues) -58: -58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue LYS50 as a starting terminus. -58: -58: Identified residue PRO65 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 228 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 233, now 232 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 634 dihedrals, 48 impropers, 419 angles -58: 597 pairs, 232 bonds and 0 virtual sites -58: -58: Total mass 1662.888 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 89 donors and 98 acceptors were found. -58: There are 129 hydrogen bonds -58: Will use HISE for residue 31 -58: Will use HISE for residue 51 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS25 HIS31 HIS51 -58: SG14 NE264 NE2226 -58: HIS31 NE264 1.921 -58: HIS51 NE2226 1.498 2.650 -58: CYS80 SG477 0.207 1.984 1.570 -58: Linking CYS-25 SG-14 and CYS-80 SG-477... -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Before cleaning: 2499 pairs -58: Before cleaning: 2631 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 58 488 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 'A' (488 atoms, 58 residues) -58: -58: Identified residue ASN24 as a starting terminus. -58: -58: Identified residue ARG81 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 58 residues with 936 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 952, now 951 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 2631 dihedrals, 208 impropers, 1704 angles -58: 2469 pairs, 951 bonds and 0 virtual sites -58: -58: Total mass 6908.576 a.m.u. -58: -58: Total charge -6.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (58 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Marked 124 virtual sites -58: Added 16 dummy masses -58: Added 26 new constraints -58: Before cleaning: 653 pairs -58: Before cleaning: 691 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 128 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (128 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 252 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 255, now 254 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 691 dihedrals, 51 impropers, 457 angles -58: 650 pairs, 254 bonds and 130 virtual sites -58: -58: Total mass 1846.132 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 30 donors and 22 acceptors were found. -58: There are 36 hydrogen bonds -58: Will use HISE for residue 29 -58: Will use HISE for residue 32 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS27 HIS29 -58: SG90 NE2111 -58: HIS29 NE2111 0.987 -58: HIS32 NE2135 1.590 1.155 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Marked 132 virtual sites -58: Added 10 dummy masses -58: Added 19 new constraints -58: Before cleaning: 748 pairs -58: Before cleaning: 788 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 149 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (149 atoms, 16 residues) -58: -58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue PHE33 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 281 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 291, now 290 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 788 dihedrals, 72 impropers, 516 angles -58: 736 pairs, 290 bonds and 133 virtual sites -58: -58: Total mass 2088.366 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 22 acceptors were found. -58: There are 26 hydrogen bonds -58: Will use HISE for residue 45 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS45 -58: NE295 -58: MET46 SD102 1.078 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Marked 123 virtual sites -58: Added 22 dummy masses -58: Added 35 new constraints -58: Before cleaning: 676 pairs -58: Before cleaning: 727 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 132 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (132 atoms, 16 residues) -58: -58: Identified residue ALA34 as a starting terminus. -58: -58: Identified residue ALA49 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 255 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 262, now 261 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 727 dihedrals, 56 impropers, 472 angles -58: 667 pairs, 261 bonds and 132 virtual sites -58: -58: Total mass 1861.124 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 21 acceptors were found. -58: There are 30 hydrogen bonds -58: Will use HISE for residue 60 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS60 -58: NE285 -58: CYS62 SG98 0.803 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Marked 111 virtual sites -58: Added 18 dummy masses -58: Added 31 new constraints -58: Before cleaning: 603 pairs -58: Before cleaning: 634 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 117 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (117 atoms, 16 residues) -58: -58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue LYS50 as a starting terminus. -58: -58: Identified residue PRO65 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 228 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 233, now 232 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 634 dihedrals, 48 impropers, 419 angles -58: 597 pairs, 232 bonds and 116 virtual sites -58: -58: Total mass 1662.888 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) -58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 89 donors and 98 acceptors were found. -58: There are 129 hydrogen bonds -58: Will use HISE for residue 31 -58: Will use HISE for residue 51 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS25 HIS31 HIS51 -58: SG14 NE264 NE2226 -58: HIS31 NE264 1.921 -58: HIS51 NE2226 1.498 2.650 -58: CYS80 SG477 0.207 1.984 1.570 -58: Linking CYS-25 SG-14 and CYS-80 SG-477... -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Marked 447 virtual sites -58: Added 58 dummy masses -58: Added 101 new constraints -58: Before cleaning: 2499 pairs -58: Before cleaning: 2631 dihedrals -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 58 488 -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 'A' (488 atoms, 58 residues) -58: -58: Identified residue ASN24 as a starting terminus. -58: -58: Identified residue ARG81 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 58 residues with 936 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 952, now 951 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 2631 dihedrals, 208 impropers, 1704 angles -58: 2469 pairs, 951 bonds and 462 virtual sites -58: -58: Total mass 6908.576 a.m.u. -58: -58: Total charge -6.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -58: -58: The Amber99sb-ildn force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) -58: [----------] 10 tests from Amber/Pdb2gmxTest (321 ms total) -58: -58: [----------] 1 test from AmberTip4p/Pdb2gmxTest -58: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/amber99sb-ildn.ff/rna.arn -58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff -58: -58: going to rename amber99sb-ildn.ff/aminoacids.r2b -58: -58: going to rename amber99sb-ildn.ff/dna.r2b -58: -58: going to rename amber99sb-ildn.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... -58: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 2 4 (only water) -58: -58: All occupancies are one -58: -58: Reading residue database... (Amber99sb-ildn) -58: -58: Processing chain 1 (4 atoms, 2 residues) -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 2 residues with 8 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 4, now 4 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 2 angles -58: 0 pairs, 4 bonds and 0 virtual sites -58: -58: Total mass 36.032 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. -58: -58: The Amber99sb-ildn force field and the tip4p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (12 ms) -58: [----------] 1 test from AmberTip4p/Pdb2gmxTest (12 ms total) -58: -58: [----------] 12 tests from Charmm/Pdb2gmxTest -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 653 pairs -58: Before cleaning: 663 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 128 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (128 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 252 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 254, now 254 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 663 dihedrals, 48 impropers, 457 angles -58: 650 pairs, 254 bonds and 0 virtual sites -58: -58: Total mass 1846.115 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 30 donors and 22 acceptors were found. -58: There are 36 hydrogen bonds -58: Will use HISE for residue 29 -58: Will use HISE for residue 32 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS27 HIS29 -58: SG90 NE2111 -58: HIS29 NE2111 0.987 -58: HIS32 NE2135 1.590 1.155 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 748 pairs -58: Before cleaning: 778 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 149 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (149 atoms, 16 residues) -58: -58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue PHE33 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus PHE-33: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 281 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 290, now 290 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 778 dihedrals, 49 impropers, 516 angles -58: 736 pairs, 290 bonds and 0 virtual sites -58: -58: Total mass 2088.361 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 22 acceptors were found. -58: There are 26 hydrogen bonds -58: Will use HISE for residue 45 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS45 -58: NE295 -58: MET46 SD102 1.078 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 676 pairs -58: Before cleaning: 696 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 132 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (132 atoms, 16 residues) -58: -58: Identified residue ALA34 as a starting terminus. -58: -58: Identified residue ALA49 as a ending terminus. -58: Start terminus ALA-34: NH3+ -58: End terminus ALA-49: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 255 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 261, now 261 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 696 dihedrals, 39 impropers, 472 angles -58: 667 pairs, 261 bonds and 0 virtual sites -58: -58: Total mass 1861.130 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 21 acceptors were found. -58: There are 30 hydrogen bonds -58: Will use HISE for residue 60 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS60 -58: NE285 -58: CYS62 SG98 0.803 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 603 pairs -58: Before cleaning: 618 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 117 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (117 atoms, 16 residues) -58: -58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue LYS50 as a starting terminus. -58: -58: Identified residue PRO65 as a ending terminus. -58: Start terminus LYS-50: NH3+ -58: End terminus PRO-65: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 228 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 232, now 232 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 618 dihedrals, 38 impropers, 419 angles -58: 597 pairs, 232 bonds and 0 virtual sites -58: -58: Total mass 1662.885 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 89 donors and 98 acceptors were found. -58: There are 129 hydrogen bonds -58: Will use HISE for residue 31 -58: Will use HISE for residue 51 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS25 HIS31 HIS51 -58: SG14 NE264 NE2226 -58: HIS31 NE264 1.921 -58: HIS51 NE2226 1.498 2.650 -58: CYS80 SG477 0.207 1.984 1.570 -58: Linking CYS-25 SG-14 and CYS-80 SG-477... -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 2499 pairs -58: Before cleaning: 2524 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 58 488 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (488 atoms, 58 residues) -58: -58: Identified residue ASN24 as a starting terminus. -58: -58: Identified residue ARG81 as a ending terminus. -58: Start terminus ASN-24: NH3+ -58: End terminus ARG-81: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 58 residues with 936 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 951, now 951 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 56 cmap torsion pairs -58: -58: There are 2524 dihedrals, 149 impropers, 1704 angles -58: 2469 pairs, 951 bonds and 0 virtual sites -58: -58: Total mass 6908.566 a.m.u. -58: -58: Total charge -6.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 39 pairs -58: Before cleaning: 39 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -58: Read 'GLU', 9 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -58: -58: chain #res #atoms -58: -58: 1 'X' 1 9 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'X' (9 atoms, 1 residues) -58: -58: Identified residue GLU1 as a starting terminus. -58: -58: Identified residue GLU1 as a ending terminus. -58: Start terminus GLU-1: NH3+ -58: End terminus GLU-1: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 1 residues with 18 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 17, now 17 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 39 dihedrals, 2 impropers, 30 angles -58: 39 pairs, 17 bonds and 0 virtual sites -58: -58: Total mass 146.123 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (12 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 124 virtual sites -58: Added 16 dummy masses -58: Added 26 new constraints -58: Before cleaning: 653 pairs -58: Before cleaning: 663 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 128 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (128 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 252 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 254, now 254 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 663 dihedrals, 48 impropers, 457 angles -58: 650 pairs, 254 bonds and 130 virtual sites -58: -58: Total mass 1846.115 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/A.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 30 donors and 22 acceptors were found. -58: There are 36 hydrogen bonds -58: Will use HISE for residue 29 -58: Will use HISE for residue 32 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS27 HIS29 -58: SG90 NE2111 -58: HIS29 NE2111 0.987 -58: HIS32 NE2135 1.590 1.155 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 132 virtual sites -58: Added 10 dummy masses -58: Added 19 new constraints -58: Before cleaning: 748 pairs -58: Before cleaning: 778 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb... -58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 149 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (149 atoms, 16 residues) -58: -58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue PHE33 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus PHE-33: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 281 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 290, now 290 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 778 dihedrals, 49 impropers, 516 angles -58: 736 pairs, 290 bonds and 133 virtual sites -58: -58: Total mass 2088.361 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/B.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 22 acceptors were found. -58: There are 26 hydrogen bonds -58: Will use HISE for residue 45 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS45 -58: NE295 -58: MET46 SD102 1.078 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 123 virtual sites -58: Added 22 dummy masses -58: Added 35 new constraints -58: Before cleaning: 676 pairs -58: Before cleaning: 696 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb... -58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 132 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (132 atoms, 16 residues) -58: -58: Identified residue ALA34 as a starting terminus. -58: -58: Identified residue ALA49 as a ending terminus. -58: Start terminus ALA-34: NH3+ -58: End terminus ALA-49: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 255 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 261, now 261 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 696 dihedrals, 39 impropers, 472 angles -58: 667 pairs, 261 bonds and 132 virtual sites -58: -58: Total mass 1861.130 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/C.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 22 donors and 21 acceptors were found. -58: There are 30 hydrogen bonds -58: Will use HISE for residue 60 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS60 -58: NE285 -58: CYS62 SG98 0.803 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 111 virtual sites -58: Added 18 dummy masses -58: Added 31 new constraints -58: Before cleaning: 603 pairs -58: Before cleaning: 618 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb... -58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms -58: -58: chain #res #atoms -58: -58: 1 ' ' 16 117 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 (117 atoms, 16 residues) -58: -58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. -58: -58: Identified residue LYS50 as a starting terminus. -58: -58: Identified residue PRO65 as a ending terminus. -58: Start terminus LYS-50: NH3+ -58: End terminus PRO-65: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 228 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 232, now 232 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 14 cmap torsion pairs -58: -58: There are 618 dihedrals, 38 impropers, 419 angles -58: 597 pairs, 232 bonds and 116 virtual sites -58: -58: Total mass 1662.885 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/D.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 89 donors and 98 acceptors were found. -58: There are 129 hydrogen bonds -58: Will use HISE for residue 31 -58: Will use HISE for residue 51 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS25 HIS31 HIS51 -58: SG14 NE264 NE2226 -58: HIS31 NE264 1.921 -58: HIS51 NE2226 1.498 2.650 -58: CYS80 SG477 0.207 1.984 1.570 -58: Linking CYS-25 SG-14 and CYS-80 SG-477... -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 447 virtual sites -58: Added 58 dummy masses -58: Added 101 new constraints -58: Before cleaning: 2499 pairs -58: Before cleaning: 2524 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb... -58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 58 488 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (488 atoms, 58 residues) -58: -58: Identified residue ASN24 as a starting terminus. -58: -58: Identified residue ARG81 as a ending terminus. -58: Start terminus ASN-24: NH3+ -58: End terminus ARG-81: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 58 residues with 936 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 951, now 951 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 56 cmap torsion pairs -58: -58: There are 2524 dihedrals, 149 impropers, 1704 angles -58: 2469 pairs, 951 bonds and 462 virtual sites -58: -58: Total mass 6908.566 a.m.u. -58: -58: Total charge -6.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/E.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) -58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Marked 8 virtual sites -58: Added 2 dummy masses -58: Added 3 new constraints -58: Before cleaning: 39 pairs -58: Before cleaning: 39 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... -58: Read 'GLU', 9 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms -58: -58: chain #res #atoms -58: -58: 1 'X' 1 9 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'X' (9 atoms, 1 residues) -58: -58: Identified residue GLU1 as a starting terminus. -58: -58: Identified residue GLU1 as a ending terminus. -58: Start terminus GLU-1: NH3+ -58: End terminus GLU-1: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 1 residues with 18 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 17, now 17 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 39 dihedrals, 2 impropers, 30 angles -58: 39 pairs, 17 bonds and 9 virtual sites -58: -58: Total mass 146.123 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (12 ms) -58: [----------] 12 tests from Charmm/Pdb2gmxTest (313 ms total) -58: -58: [----------] 8 tests from ChainSep/Pdb2gmxTest -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 651 pairs -58: Before cleaning: 661 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on changing chain id only (ignoring TER records). -58: -58: Merged chains into joint molecule definitions at 2 places. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 16 127 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (127 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue GLU5 as a ending terminus. -58: -58: Identified residue PHE6 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus GLU-5: COO- -58: Start terminus PHE-6: NH3+ -58: End terminus MET-12: COO- -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 258 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 258, now 258 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 10 cmap torsion pairs -58: -58: There are 661 dihedrals, 46 impropers, 463 angles -58: 648 pairs, 258 bonds and 0 virtual sites -58: -58: Total mass 1882.146 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (22 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 123 pairs -58: Before cleaning: 123 dihedrals -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 10 donors and 7 acceptors were found. -58: There are 7 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: HIS8 -58: NE223 -58: MET12 SD55 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 317 pairs -58: Before cleaning: 322 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 211 pairs -58: Before cleaning: 216 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on changing chain id only (ignoring TER records). -58: -58: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 4 28 -58: -58: 2 'B' 7 58 -58: -58: 3 'C' 5 41 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (28 atoms, 4 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue GLU5 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus GLU-5: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 4 residues with 51 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 50, now 50 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 2 cmap torsion pairs -58: -58: There are 123 dihedrals, 9 impropers, 88 angles -58: 123 pairs, 50 bonds and 0 virtual sites -58: -58: Total mass 434.421 a.m.u. -58: -58: Total charge -2.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (58 atoms, 7 residues) -58: -58: Identified residue PHE6 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: Start terminus PHE-6: NH3+ -58: End terminus MET-12: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 7 residues with 124 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 125, now 125 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 5 cmap torsion pairs -58: -58: There are 322 dihedrals, 19 impropers, 227 angles -58: 314 pairs, 125 bonds and 0 virtual sites -58: -58: Total mass 846.083 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Processing chain 3 'C' (41 atoms, 5 residues) -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 5 residues with 83 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 83, now 83 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 3 cmap torsion pairs -58: -58: There are 216 dihedrals, 18 impropers, 148 angles -58: 211 pairs, 83 bonds and 0 virtual sites -58: -58: Total mass 601.643 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 51 atoms 4 residues -58: -58: Including chain 2 in system: 124 atoms 7 residues -58: -58: Including chain 3 in system: 83 atoms 5 residues -58: -58: Now there are 258 atoms and 16 residues -58: -58: Total mass in system 1882.146 a.m.u. -58: -58: Total charge in system 0.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (21 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 651 pairs -58: Before cleaning: 661 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records only (ignoring chain id). -58: -58: Merged chains into joint molecule definitions at 2 places. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 16 127 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (127 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ILE9 as a ending terminus. -58: -58: Identified residue LYS10 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ILE-9: COO- -58: Start terminus LYS-10: NH3+ -58: End terminus MET-12: COO- -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 258 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 258, now 258 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 10 cmap torsion pairs -58: -58: There are 661 dihedrals, 46 impropers, 463 angles -58: 648 pairs, 258 bonds and 0 virtual sites -58: -58: Total mass 1882.146 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 10 donors and 12 acceptors were found. -58: There are 13 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 -58: SG9 -58: HIS8 NE251 1.055 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 288 pairs -58: Before cleaning: 293 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 152 pairs -58: Before cleaning: 152 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 211 pairs -58: Before cleaning: 216 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records only (ignoring chain id). -58: -58: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 8 61 -58: -58: 2 'B' 3 25 -58: -58: 3 'C' 5 41 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (61 atoms, 8 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ILE9 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ILE-9: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 8 residues with 114 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 115, now 115 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 6 cmap torsion pairs -58: -58: There are 293 dihedrals, 23 impropers, 203 angles -58: 285 pairs, 115 bonds and 0 virtual sites -58: -58: Total mass 888.952 a.m.u. -58: -58: Total charge -2.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (25 atoms, 3 residues) -58: -58: Identified residue LYS10 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: Start terminus LYS-10: NH3+ -58: End terminus MET-12: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 61 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 60, now 60 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 152 dihedrals, 5 impropers, 112 angles -58: 152 pairs, 60 bonds and 0 virtual sites -58: -58: Total mass 391.552 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Processing chain 3 'C' (41 atoms, 5 residues) -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 5 residues with 83 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 83, now 83 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 3 cmap torsion pairs -58: -58: There are 216 dihedrals, 18 impropers, 148 angles -58: 211 pairs, 83 bonds and 0 virtual sites -58: -58: Total mass 601.643 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 114 atoms 8 residues -58: -58: Including chain 2 in system: 61 atoms 3 residues -58: -58: Including chain 3 in system: 83 atoms 5 residues -58: -58: Now there are 258 atoms and 16 residues -58: -58: Total mass in system 1882.146 a.m.u. -58: -58: Total charge in system 0.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 650 pairs -58: Before cleaning: 660 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: Merged chains into joint molecule definitions at 3 places. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 16 127 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (127 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue GLU5 as a ending terminus. -58: -58: Identified residue PHE6 as a starting terminus. -58: -58: Identified residue ILE9 as a ending terminus. -58: -58: Identified residue LYS10 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus GLU-5: COO- -58: Start terminus PHE-6: NH3+ -58: End terminus ILE-9: COO- -58: Start terminus LYS-10: NH3+ -58: End terminus MET-12: COO- -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 261 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 260, now 260 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 8 cmap torsion pairs -58: -58: There are 660 dihedrals, 45 impropers, 466 angles -58: 647 pairs, 260 bonds and 0 virtual sites -58: -58: Total mass 1900.162 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (22 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -58: -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 123 pairs -58: Before cleaning: 123 dihedrals -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 6 donors and 4 acceptors were found. -58: There are 3 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 164 pairs -58: Before cleaning: 169 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 152 pairs -58: Before cleaning: 152 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 211 pairs -58: Before cleaning: 216 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -58: -58: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 4 28 -58: -58: 2 'B' 4 33 -58: -58: 3 'B' 3 25 -58: -58: 4 'C' 5 41 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (28 atoms, 4 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue GLU5 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus GLU-5: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 4 residues with 51 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 50, now 50 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 2 cmap torsion pairs -58: -58: There are 123 dihedrals, 9 impropers, 88 angles -58: 123 pairs, 50 bonds and 0 virtual sites -58: -58: Total mass 434.421 a.m.u. -58: -58: Total charge -2.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (33 atoms, 4 residues) -58: -58: Identified residue PHE6 as a starting terminus. -58: -58: Identified residue ILE9 as a ending terminus. -58: Start terminus PHE-6: NH3+ -58: End terminus ILE-9: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 4 residues with 66 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 67, now 67 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 2 cmap torsion pairs -58: -58: There are 169 dihedrals, 13 impropers, 118 angles -58: 161 pairs, 67 bonds and 0 virtual sites -58: -58: Total mass 472.547 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Processing chain 3 'B' (25 atoms, 3 residues) -58: -58: Identified residue LYS10 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: Start terminus LYS-10: NH3+ -58: End terminus MET-12: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 61 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 60, now 60 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 152 dihedrals, 5 impropers, 112 angles -58: 152 pairs, 60 bonds and 0 virtual sites -58: -58: Total mass 391.552 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Processing chain 4 'C' (41 atoms, 5 residues) -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 5 residues with 83 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 83, now 83 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 3 cmap torsion pairs -58: -58: There are 216 dihedrals, 18 impropers, 148 angles -58: 211 pairs, 83 bonds and 0 virtual sites -58: -58: Total mass 601.643 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 51 atoms 4 residues -58: -58: Including chain 2 in system: 66 atoms 4 residues -58: -58: Including chain 3 in system: 61 atoms 3 residues -58: -58: Including chain 4 in system: 83 atoms 5 residues -58: -58: Now there are 261 atoms and 16 residues -58: -58: Total mass in system 1900.162 a.m.u. -58: -58: Total charge in system 0.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (20 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 25 donors and 23 acceptors were found. -58: There are 41 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 652 pairs -58: Before cleaning: 662 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records and chain id changing. -58: -58: Merged chains into joint molecule definitions at 1 places. -58: -58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 16 127 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (127 atoms, 16 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus MET-12: COO- -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 255 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 256, now 256 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 12 cmap torsion pairs -58: -58: There are 662 dihedrals, 47 impropers, 460 angles -58: 649 pairs, 256 bonds and 0 virtual sites -58: -58: Total mass 1864.131 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) -58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: Analysing hydrogen-bonding network for automated assignment of histidine -58: protonation. 14 donors and 15 acceptors were found. -58: There are 20 hydrogen bonds -58: Will use HISE for residue 8 -58: 9 out of 9 lines of specbond.dat converted successfully -58: Special Atom Distance matrix: -58: CYS3 HIS8 -58: SG9 NE251 -58: HIS8 NE251 1.055 -58: MET12 SD83 0.763 0.990 -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 441 pairs -58: Before cleaning: 446 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 211 pairs -58: Before cleaning: 216 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... -58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records and chain id changing. -58: -58: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 11 86 -58: -58: 2 'C' 5 41 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (86 atoms, 11 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue MET12 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus MET-12: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 11 residues with 172 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 173, now 173 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 9 cmap torsion pairs -58: -58: There are 446 dihedrals, 29 impropers, 312 angles -58: 438 pairs, 173 bonds and 0 virtual sites -58: -58: Total mass 1262.488 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'C' (41 atoms, 5 residues) -58: -58: Identified residue ASN13 as a starting terminus. -58: -58: Identified residue SER17 as a ending terminus. -58: Start terminus ASN-13: NH3+ -58: End terminus SER-17: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 5 residues with 83 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 83, now 83 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 3 cmap torsion pairs -58: -58: There are 216 dihedrals, 18 impropers, 148 angles -58: 211 pairs, 83 bonds and 0 virtual sites -58: -58: Total mass 601.643 a.m.u. -58: -58: Total charge 1.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 172 atoms 11 residues -58: -58: Including chain 2 in system: 83 atoms 5 residues -58: -58: Now there are 255 atoms and 16 residues -58: -58: Total mass in system 1864.131 a.m.u. -58: -58: Total charge in system 0.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) -58: [----------] 8 tests from ChainSep/Pdb2gmxTest (167 ms total) -58: -58: [----------] 4 tests from ChainChanges/Pdb2gmxTest -58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 83 pairs -58: Before cleaning: 83 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 145 pairs -58: Before cleaning: 150 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -58: Read 'Fragments of peptides and ions', 47 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on changing chain id only (ignoring TER records). -58: -58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 3 19 -58: -58: 2 'B' 3 28 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (19 atoms, 3 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ASP4 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ASP-4: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 36 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 35, now 35 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 83 dihedrals, 6 impropers, 61 angles -58: 83 pairs, 35 bonds and 0 virtual sites -58: -58: Total mass 306.314 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (28 atoms, 3 residues) -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue TRP20 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus TRP-20: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 57 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 58, now 58 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 150 dihedrals, 5 impropers, 103 angles -58: 142 pairs, 58 bonds and 0 virtual sites -58: -58: Total mass 404.468 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 36 atoms 3 residues -58: -58: Including chain 2 in system: 57 atoms 3 residues -58: -58: Now there are 93 atoms and 6 residues -58: -58: Total mass in system 710.782 a.m.u. -58: -58: Total charge in system -1.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (13 ms) -58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 83 pairs -58: Before cleaning: 83 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 145 pairs -58: Before cleaning: 150 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -58: Read 'Fragments of peptides and ions', 47 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records only (ignoring chain id). -58: -58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 3 19 -58: -58: 2 'B' 3 28 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (19 atoms, 3 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ASP4 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ASP-4: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 36 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 35, now 35 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 83 dihedrals, 6 impropers, 61 angles -58: 83 pairs, 35 bonds and 0 virtual sites -58: -58: Total mass 306.314 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (28 atoms, 3 residues) -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue TRP20 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus TRP-20: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 57 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 58, now 58 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 150 dihedrals, 5 impropers, 103 angles -58: 142 pairs, 58 bonds and 0 virtual sites -58: -58: Total mass 404.468 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 36 atoms 3 residues -58: -58: Including chain 2 in system: 57 atoms 3 residues -58: -58: Now there are 93 atoms and 6 residues -58: -58: Total mass in system 710.782 a.m.u. -58: -58: Total charge in system -1.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (16 ms) -58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 83 pairs -58: Before cleaning: 83 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 145 pairs -58: Before cleaning: 150 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -58: Read 'Fragments of peptides and ions', 47 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 3 19 -58: -58: 2 'B' 3 28 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (19 atoms, 3 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ASP4 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ASP-4: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 36 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 35, now 35 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 83 dihedrals, 6 impropers, 61 angles -58: 83 pairs, 35 bonds and 0 virtual sites -58: -58: Total mass 306.314 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (28 atoms, 3 residues) -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue TRP20 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus TRP-20: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 57 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 58, now 58 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 150 dihedrals, 5 impropers, 103 angles -58: 142 pairs, 58 bonds and 0 virtual sites -58: -58: Total mass 404.468 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 36 atoms 3 residues -58: -58: Including chain 2 in system: 57 atoms 3 residues -58: -58: Now there are 93 atoms and 6 residues -58: -58: Total mass in system 710.782 a.m.u. -58: -58: Total charge in system -1.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) -58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 83 pairs -58: Before cleaning: 83 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 145 pairs -58: Before cleaning: 150 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... -58: Read 'Fragments of peptides and ions', 47 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records and chain id changing. -58: -58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 3 19 -58: -58: 2 'B' 3 28 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (19 atoms, 3 residues) -58: -58: Identified residue ALA2 as a starting terminus. -58: -58: Identified residue ASP4 as a ending terminus. -58: Start terminus ALA-2: NH3+ -58: End terminus ASP-4: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 36 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 35, now 35 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 83 dihedrals, 6 impropers, 61 angles -58: 83 pairs, 35 bonds and 0 virtual sites -58: -58: Total mass 306.314 a.m.u. -58: -58: Total charge -1.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'B' (28 atoms, 3 residues) -58: -58: Identified residue THR18 as a starting terminus. -58: -58: Identified residue TRP20 as a ending terminus. -58: Start terminus THR-18: NH3+ -58: End terminus TRP-20: COO- -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 3 residues with 57 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 58, now 58 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 1 cmap torsion pairs -58: -58: There are 150 dihedrals, 5 impropers, 103 angles -58: 142 pairs, 58 bonds and 0 virtual sites -58: -58: Total mass 404.468 a.m.u. -58: -58: Total charge -0.000 e -58: -58: Writing topology -58: -58: Including chain 1 in system: 36 atoms 3 residues -58: -58: Including chain 2 in system: 57 atoms 3 residues -58: -58: Now there are 93 atoms and 6 residues -58: -58: Total mass in system 710.782 a.m.u. -58: -58: Total charge in system -1.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (14 ms) -58: [----------] 4 tests from ChainChanges/Pdb2gmxTest (58 ms total) -58: -58: [----------] 4 tests from Cyclic/Pdb2gmxTest -58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: WARNING: all CONECT records are ignored -58: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -58: -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 6040 pairs -58: Before cleaning: 6605 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 6040 pairs -58: Before cleaning: 6605 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -58: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. -58: -58: Moved all the water blocks to the end -58: -58: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms -58: -58: chain #res #atoms -58: -58: 1 'P' 71 1527 -58: -58: 2 'Q' 71 1527 -58: -58: 3 'Q' 7 7 -58: -58: 4 ' ' 10 10 (only water) -58: -58: 5 ' ' 16 16 (only water) -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'P' (1527 atoms, 71 residues) -58: -58: Identified residue G1 as a starting terminus. -58: -58: Identified residue U71 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 71 residues with 2297 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 2481, now 2481 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 6605 dihedrals, 183 impropers, 4434 angles -58: 5827 pairs, 2481 bonds and 0 virtual sites -58: -58: Total mass 22984.514 a.m.u. -58: -58: Total charge -71.000 e -58: -58: Writing topology -58: -58: Processing chain 2 'Q' (1527 atoms, 71 residues) -58: -58: Identified residue G1 as a starting terminus. -58: -58: Identified residue U71 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 71 residues with 2297 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: Number of bonds was 2481, now 2481 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 6605 dihedrals, 183 impropers, 4434 angles -58: 5827 pairs, 2481 bonds and 0 virtual sites -58: -58: Total mass 22984.514 a.m.u. -58: -58: Total charge -71.000 e -58: -58: Writing topology -58: -58: Processing chain 3 'Q' (7 atoms, 7 residues) -58: -58: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -58: -58: Disabling further notes about ions. -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 7 residues with 7 atoms -58: Chain time... -58: -58: Making bonds... -58: -58: No bonds -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 0 angles -58: 0 pairs, 0 bonds and 0 virtual sites -58: -58: Total mass 170.135 a.m.u. -58: -58: Total charge 14.000 e -58: -58: Writing topology -58: -58: Processing chain 4 (10 atoms, 10 residues) -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 10 residues with 30 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 30, now 30 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 30 angles -58: 0 pairs, 30 bonds and 0 virtual sites -58: -58: Total mass 180.154 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Processing chain 5 (16 atoms, 16 residues) -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 48 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 48, now 48 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 48 angles -58: 0 pairs, 48 bonds and 0 virtual sites -58: -58: Total mass 288.246 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Including chain 1 in system: 2297 atoms 71 residues -58: -58: Including chain 2 in system: 2297 atoms 71 residues -58: -58: Including chain 3 in system: 7 atoms 7 residues -58: -58: Including chain 4 in system: 30 atoms 10 residues -58: -58: Including chain 5 in system: 48 atoms 16 residues -58: -58: Now there are 4679 atoms and 175 residues -58: -58: Total mass in system 46607.562 a.m.u. -58: -58: Total charge in system -128.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (176 ms) -58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 2325 pairs -58: Before cleaning: 2325 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -58: Read 'CARNOCYCLIN-A', 413 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 60 413 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (413 atoms, 60 residues) -58: -58: Identified residue LEU1 as a starting terminus. -58: -58: Identified residue LEU60 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 60 residues with 878 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 880, now 880 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 60 cmap torsion pairs -58: -58: There are 2325 dihedrals, 137 impropers, 1614 angles -58: 2319 pairs, 880 bonds and 0 virtual sites -58: -58: Total mass 5866.087 a.m.u. -58: -58: Total charge 4.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (45 ms) -58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: WARNING: all CONECT records are ignored -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 12080 pairs -58: Before cleaning: 13210 dihedrals -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... -58: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: Moved all the water blocks to the end -58: -58: Merged chains into joint molecule definitions at 2 places. -58: -58: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms -58: -58: chain #res #atoms -58: -58: 1 'P' 149 3061 -58: -58: 2 ' ' 10 10 (only water) -58: -58: 3 ' ' 16 16 (only water) -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'P' (3061 atoms, 149 residues) -58: -58: Identified residue G1 as a starting terminus. -58: -58: Identified residue U71 as a ending terminus. -58: -58: Identified residue G1 as a starting terminus. -58: -58: Identified residue U71 as a ending terminus. -58: -58: Residue MG72 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG73 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG74 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG75 has type 'Ion', assuming it is not linked into a chain. -58: -58: Residue MG76 has type 'Ion', assuming it is not linked into a chain. -58: -58: Disabling further notes about ions. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 149 residues with 4601 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 4962, now 4962 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 13210 dihedrals, 366 impropers, 8868 angles -58: 11654 pairs, 4962 bonds and 0 virtual sites -58: -58: Total mass 46139.162 a.m.u. -58: -58: Total charge -128.000 e -58: -58: Writing topology -58: -58: Processing chain 2 (10 atoms, 10 residues) -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 10 residues with 30 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 30, now 30 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 30 angles -58: 0 pairs, 30 bonds and 0 virtual sites -58: -58: Total mass 180.154 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Processing chain 3 (16 atoms, 16 residues) -58: -58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 16 residues with 48 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 48, now 48 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 0 dihedrals, 0 impropers, 48 angles -58: 0 pairs, 48 bonds and 0 virtual sites -58: -58: Total mass 288.246 a.m.u. -58: -58: Total charge 0.000 e -58: -58: Including chain 1 in system: 4601 atoms 149 residues -58: -58: Including chain 2 in system: 30 atoms 10 residues -58: -58: Including chain 3 in system: 48 atoms 16 residues -58: -58: Now there are 4679 atoms and 175 residues -58: -58: Total mass in system 46607.562 a.m.u. -58: -58: Total charge in system -128.000 e -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (261 ms) -58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.r2b -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.r2b -58: All occupancies are one -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/atomtypes.atp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.rtp -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/lipids.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.hdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.n.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.c.tdb -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.c.tdb -58: 9 out of 9 lines of specbond.dat converted successfully -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/aminoacids.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/dna.arn -58: Opening force field file /build/reproducible-path/gromacs-2025.3/share/top/charmm27.ff/rna.arn -58: Before cleaning: 2325 pairs -58: Before cleaning: 2325 dihedrals -58: Using the Charmm27 force field in directory charmm27.ff -58: -58: going to rename charmm27.ff/aminoacids.r2b -58: -58: going to rename charmm27.ff/rna.r2b -58: Reading /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... -58: Read 'CARNOCYCLIN-A', 413 atoms -58: -58: Analyzing pdb file -58: Splitting chemical chains based on TER records or chain id changing. -58: -58: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms -58: -58: chain #res #atoms -58: -58: 1 'A' 60 413 -58: -58: All occupancies are one -58: -58: Reading residue database... (Charmm27) -58: -58: Processing chain 1 'A' (413 atoms, 60 residues) -58: -58: Identified residue LEU1 as a starting terminus. -58: -58: Identified residue LEU60 as a ending terminus. -58: -58: Checking for duplicate atoms.... -58: -58: Generating any missing hydrogen atoms and/or adding termini. -58: -58: Now there are 60 residues with 878 atoms -58: -58: Making bonds... -58: -58: Number of bonds was 880, now 880 -58: -58: Generating angles, dihedrals and pairs... -58: -58: Making cmap torsions... -58: -58: There are 60 cmap torsion pairs -58: -58: There are 2325 dihedrals, 137 impropers, 1614 angles -58: 2319 pairs, 880 bonds and 0 virtual sites -58: -58: Total mass 5866.087 a.m.u. -58: -58: Total charge 4.000 e -58: -58: Writing topology -58: -58: Writing coordinate file... -58: -58: --------- PLEASE NOTE ------------ -58: -58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. -58: -58: The Charmm27 force field and the tip3p water model are used. -58: -58: --------- ETON ESAELP ------------ -58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (47 ms) -58: [----------] 4 tests from Cyclic/Pdb2gmxTest (531 ms total) -58: -58: [----------] Global test environment tear-down -58: [==========] 39 tests from 6 test suites ran. (1405 ms total) -58: [ PASSED ] 39 tests. -58/96 Test #58: Pdb2gmx3Test ................................. Passed 1.60 sec -test 59 - Start 59: CorrelationsTest - -59: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/CorrelationsTest.xml" -59: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/correlationfunctions/tests -59: Test timeout computed to be: 30 -59: [==========] Running 21 tests from 3 test suites. -59: [----------] Global test environment set-up. -59: [----------] 10 tests from AutocorrTest -59: [ RUN ] AutocorrTest.EacNormal -59: [ OK ] AutocorrTest.EacNormal (36 ms) -59: [ RUN ] AutocorrTest.EacNoNormalize -59: [ OK ] AutocorrTest.EacNoNormalize (22 ms) -59: [ RUN ] AutocorrTest.EacCos -59: [ OK ] AutocorrTest.EacCos (48 ms) -59: [ RUN ] AutocorrTest.EacVector -59: [ OK ] AutocorrTest.EacVector (70 ms) -59: [ RUN ] AutocorrTest.EacRcross -59: [ OK ] AutocorrTest.EacRcross (1 ms) -59: [ RUN ] AutocorrTest.EacP0 -59: [ OK ] AutocorrTest.EacP0 (70 ms) -59: [ RUN ] AutocorrTest.EacP1 -59: [ OK ] AutocorrTest.EacP1 (70 ms) -59: [ RUN ] AutocorrTest.EacP2 -59: [ OK ] AutocorrTest.EacP2 (142 ms) -59: [ RUN ] AutocorrTest.EacP3 -59: [ OK ] AutocorrTest.EacP3 (2 ms) -59: [ RUN ] AutocorrTest.EacP4 -59: [ OK ] AutocorrTest.EacP4 (66 ms) -59: [----------] 10 tests from AutocorrTest (533 ms total) -59: -59: [----------] 10 tests from ExpfitTest -59: [ RUN ] ExpfitTest.EffnEXP1 -59: [ OK ] ExpfitTest.EffnEXP1 (0 ms) -59: [ RUN ] ExpfitTest.EffnEXP2 -59: [ OK ] ExpfitTest.EffnEXP2 (0 ms) -59: [ RUN ] ExpfitTest.EffnEXPEXP -59: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) -59: [ RUN ] ExpfitTest.EffnEXP5 -59: [ OK ] ExpfitTest.EffnEXP5 (2 ms) -59: [ RUN ] ExpfitTest.EffnEXP7 -59: [ OK ] ExpfitTest.EffnEXP7 (1 ms) -59: [ RUN ] ExpfitTest.EffnEXP9 -59: [ OK ] ExpfitTest.EffnEXP9 (8 ms) -59: [ RUN ] ExpfitTest.EffnERF -59: [ OK ] ExpfitTest.EffnERF (1 ms) -59: [ RUN ] ExpfitTest.EffnERREST -59: [ OK ] ExpfitTest.EffnERREST (1 ms) -59: [ RUN ] ExpfitTest.EffnVAC -59: [ OK ] ExpfitTest.EffnVAC (3 ms) -59: [ RUN ] ExpfitTest.EffnPRES -59: [ OK ] ExpfitTest.EffnPRES (8 ms) -59: [----------] 10 tests from ExpfitTest (28 ms total) -59: -59: [----------] 1 test from ManyAutocorrelationTest -59: [ RUN ] ManyAutocorrelationTest.Empty -59: [ OK ] ManyAutocorrelationTest.Empty (0 ms) -59: [----------] 1 test from ManyAutocorrelationTest (0 ms total) -59: -59: [----------] Global test environment tear-down -59: [==========] 21 tests from 3 test suites ran. (565 ms total) -59: [ PASSED ] 21 tests. -59/96 Test #59: CorrelationsTest ............................. Passed 0.76 sec -test 60 - Start 60: AnalysisDataUnitTests - -60: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" -60: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/analysisdata/tests -60: Test timeout computed to be: 30 -60: [==========] Running 69 tests from 14 test suites. -60: [----------] Global test environment set-up. -60: [----------] 3 tests from AnalysisDataInitializationTest -60: [ RUN ] AnalysisDataInitializationTest.BasicInitialization -60: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) -60: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules -60: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) -60: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules -60: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) -60: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) -60: -60: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData -60: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly -60: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames -60: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks -60: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData -60: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) -60: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks -60: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) -60: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) -60: -60: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData -60: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly -60: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames -60: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks -60: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData -60: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) -60: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks -60: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) -60: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) -60: -60: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData -60: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly -60: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames -60: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks -60: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData -60: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) -60: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks -60: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) -60: [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) -60: -60: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData -60: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly -60: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly -60: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames -60: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks -60: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData -60: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) -60: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks -60: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) -60: [----------] 8 tests from AnalysisDataCommonTest/3 (2 ms total) -60: -60: [----------] 4 tests from AnalysisArrayDataTest -60: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly -60: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) -60: [ RUN ] AnalysisArrayDataTest.StorageWorks -60: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) -60: [ RUN ] AnalysisArrayDataTest.CanSetXAxis -60: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) -60: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount -60: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) -60: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) -60: -60: [----------] 6 tests from AverageModuleTest -60: [ RUN ] AverageModuleTest.BasicTest -60: [ OK ] AverageModuleTest.BasicTest (0 ms) -60: [ RUN ] AverageModuleTest.HandlesMultipointData -60: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) -60: [ RUN ] AverageModuleTest.HandlesMultipleDataSets -60: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) -60: [ RUN ] AverageModuleTest.HandlesDataSetAveraging -60: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) -60: [ RUN ] AverageModuleTest.CanCustomizeXAxis -60: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) -60: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis -60: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) -60: [----------] 6 tests from AverageModuleTest (2 ms total) -60: -60: [----------] 2 tests from FrameAverageModuleTest -60: [ RUN ] FrameAverageModuleTest.BasicTest -60: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) -60: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets -60: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) -60: [----------] 2 tests from FrameAverageModuleTest (0 ms total) -60: -60: [----------] 7 tests from AnalysisHistogramSettingsTest -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) -60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange -60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) -60: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) -60: -60: [----------] 2 tests from SimpleHistogramModuleTest -60: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly -60: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) -60: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll -60: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -60: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) -60: -60: [----------] 3 tests from WeightedHistogramModuleTest -60: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly -60: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) -60: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll -60: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) -60: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets -60: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) -60: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) -60: -60: [----------] 3 tests from BinAverageModuleTest -60: [ RUN ] BinAverageModuleTest.ComputesCorrectly -60: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) -60: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll -60: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) -60: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets -60: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) -60: [----------] 3 tests from BinAverageModuleTest (1 ms total) -60: -60: [----------] 4 tests from AbstractAverageHistogramTest -60: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly -60: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) -60: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram -60: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) -60: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth -60: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) -60: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins -60: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) -60: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) -60: -60: [----------] 3 tests from LifetimeModuleTest -60: [ RUN ] LifetimeModuleTest.BasicTest -60: [ OK ] LifetimeModuleTest.BasicTest (0 ms) -60: [ RUN ] LifetimeModuleTest.CumulativeTest -60: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) -60: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets -60: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) -60: [----------] 3 tests from LifetimeModuleTest (1 ms total) -60: -60: [----------] Global test environment tear-down -60: [==========] 69 tests from 14 test suites ran. (20 ms total) -60: [ PASSED ] 69 tests. -60/96 Test #60: AnalysisDataUnitTests ........................ Passed 0.21 sec -test 61 - Start 61: CoordinateIOTests - -61: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/CoordinateIOTests.xml" -61: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/coordinateio/tests -61: Test timeout computed to be: 30 -61: [==========] Running 67 tests from 20 test suites. -61: [----------] Global test environment set-up. -61: [----------] 1 test from OutputSelectorDeathTest -61: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (1 ms) -61: [----------] 1 test from OutputSelectorDeathTest (1 ms total) -61: -61: [----------] 5 tests from TrajectoryFrameWriterTest -61: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) -61: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) -61: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) -61: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (2 ms) -61: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks -61: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) -61: [----------] 5 tests from TrajectoryFrameWriterTest (7 ms total) -61: -61: [----------] 5 tests from OutputAdapterContainer -61: [ RUN ] OutputAdapterContainer.MakeEmpty -61: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) -61: [ RUN ] OutputAdapterContainer.AddAdapter -61: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) -61: [ RUN ] OutputAdapterContainer.RejectBadAdapter -61: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) -61: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter -61: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) -61: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters -61: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) -61: [----------] 5 tests from OutputAdapterContainer (0 ms total) -61: -61: [----------] 3 tests from RegisterFrameConverterTest -61: [ RUN ] RegisterFrameConverterTest.NoConverterWorks -61: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) -61: [ RUN ] RegisterFrameConverterTest.RegistrationWorks -61: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) -61: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees -61: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) -61: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) -61: -61: [----------] 5 tests from FlagTest -61: [ RUN ] FlagTest.CanSetSimpleFlag -61: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) -61: [ RUN ] FlagTest.CanAddNewBox -61: [ OK ] FlagTest.CanAddNewBox (0 ms) -61: [ RUN ] FlagTest.SetsImplicitPrecisionChange -61: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) -61: [ RUN ] FlagTest.SetsImplicitStartTimeChange -61: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) -61: [ RUN ] FlagTest.SetsImplicitTimeStepChange -61: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) -61: [----------] 5 tests from FlagTest (0 ms total) -61: -61: [----------] 5 tests from SetAtomsTest -61: [ RUN ] SetAtomsTest.RemovesExistingAtoms -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) -61: [ RUN ] SetAtomsTest.AddsNewAtoms -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) -61: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) -61: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) -61: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) -61: [----------] 5 tests from SetAtomsTest (6 ms total) -61: -61: [----------] 2 tests from SetBothTimeTest -61: [ RUN ] SetBothTimeTest.StartTimeZeroWorks -61: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) -61: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks -61: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) -61: [----------] 2 tests from SetBothTimeTest (0 ms total) -61: -61: [----------] 2 tests from SetStartTimeTest -61: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart -61: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) -61: [ RUN ] SetStartTimeTest.WorksWithZeroStart -61: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) -61: [----------] 2 tests from SetStartTimeTest (0 ms total) -61: -61: [----------] 1 test from SetTimeStepTest -61: [ RUN ] SetTimeStepTest.SetTimeStepWorks -61: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) -61: [----------] 1 test from SetTimeStepTest (0 ms total) -61: -61: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) -61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) -61: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (7 ms total) -61: -61: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles -61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) -61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) -61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) -61: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (3 ms total) -61: -61: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles -61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 -61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) -61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 -61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) -61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 -61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) -61: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) -61: -61: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles -61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) -61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) -61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) -61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) -61: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (10 ms total) -61: -61: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles -61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) -61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) -61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) -61: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (3 ms total) -61: -61: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles -61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 -61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) -61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 -61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) -61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 -61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) -61: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) -61: -61: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles -61: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) -61: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) -61: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) -61: -61: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles -61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 -61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) -61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 -61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) -61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 -61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) -61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 -61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) -61: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) -61: -61: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles -61: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) -61: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) -61: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) -61: -61: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles -61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 -61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) -61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 -61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) -61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 -61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) -61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 -61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) -61: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) -61: -61: [----------] 4 tests from ModuleSupported/NoOptionalOutput -61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) -61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) -61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) -61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 -61: -61: WARNING: Masses and atomic (Van der Waals) radii will be guessed -61: based on residue and atom names, since they could not be -61: definitively assigned from the information in your input -61: files. These guessed numbers might deviate from the mass -61: and radius of the atom type. Please check the output -61: files if necessary. Note, that this functionality may -61: be removed in a future GROMACS version. Please, consider -61: using another file format for your input. -61: -61: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) -61: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) -61: -61: [----------] Global test environment tear-down -61: [==========] 67 tests from 20 test suites ran. (53 ms total) -61: [ PASSED ] 67 tests. -61/96 Test #61: CoordinateIOTests ............................ Passed 0.24 sec -test 62 - Start 62: TrajectoryAnalysisUnitTests - -62: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" -62: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests -62: Test timeout computed to be: 1920 -62: [==========] Running 393 tests from 21 test suites. -62: [----------] Global test environment set-up. -62: [----------] 11 tests from AngleModuleTest -62: [ RUN ] AngleModuleTest.ComputesSimpleAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) -62: [ RUN ] AngleModuleTest.ComputesDihedrals -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) -62: [ RUN ] AngleModuleTest.ComputesVectorPairAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) -62: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) -62: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) -62: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) -62: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles -62: Reading frames from gro file 'Test system for different angles', 33 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) -62: [ RUN ] AngleModuleTest.ComputesMultipleAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) -62: [ RUN ] AngleModuleTest.HandlesDynamicSelections -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) -62: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) -62: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) -62: [----------] 11 tests from AngleModuleTest (17 ms total) -62: -62: [----------] 5 tests from ClustsizeTest -62: [ RUN ] ClustsizeTest.NoMolDefaultCutoff -62: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -62: There is one group in the index -62: '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Total number of atoms in clusters = 24 -62: cmid: 2, cmax: 4, max_size: 6 -62: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -62: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) -62: [ RUN ] ClustsizeTest.NoMolShortCutoff -62: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements -62: There is one group in the index -62: '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Total number of atoms in clusters = 24 -62: cmid: 1, cmax: 6, max_size: 6 -62: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 -62: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (2 ms) -62: [ RUN ] ClustsizeTest.MolDefaultCutoff -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Total number of atoms in clusters = 8 -62: cmid: 2, cmax: 4, max_size: 2 -62: 50%100%cmid: 2, cmax: 6, max_size: 2 -62: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (3 ms) -62: [ RUN ] ClustsizeTest.MolShortCutoff -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Total number of atoms in clusters = 8 -62: cmid: 1, cmax: 6, max_size: 2 -62: 50%100%cmid: 2, cmax: 6, max_size: 2 -62: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) -62: [ RUN ] ClustsizeTest.MolCSize -62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Total number of atoms in clusters = 8 -62: cmid: 2, cmax: 4, max_size: 2 -62: 50%100%cmid: 2, cmax: 6, max_size: 2 -62: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) -62: [----------] 5 tests from ClustsizeTest (10 ms total) -62: -62: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest -62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp -62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) -62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory -62: Reading frames from gro file 'Test system', 8 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (1 ms) -62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset -62: Reading frames from gro file 'Test system', 8 atoms. -62: Reading frame 0 time 0.000 -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) -62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory -62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) -62: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) -62: -62: [----------] 4 tests from ConvertTrjModuleTest -62: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading frame 0 time 0.000 Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (6 ms) -62: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading frame 0 time 0.000 Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) -62: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) -62: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms -62: Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) -62: [----------] 4 tests from ConvertTrjModuleTest (15 ms total) -62: -62: [----------] 6 tests from DistanceModuleTest -62: [ RUN ] DistanceModuleTest.ComputesDistances -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: atomname S1 S2: -62: Number of samples: 5 -62: Average distance: 1.43246 nm -62: Standard deviation: 0.96700 nm -62: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) -62: [ RUN ] DistanceModuleTest.ComputesMultipleDistances -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: atomname S1 S2: -62: Number of samples: 5 -62: Average distance: 1.43246 nm -62: Standard deviation: 0.96700 nm -62: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: -62: Number of samples: 4 -62: Average distance: 1.81066 nm -62: Standard deviation: 0.79289 nm -62: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) -62: [ RUN ] DistanceModuleTest.HandlesDynamicSelections -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: atomname S1 S2 and res_cog x < 2.8: -62: Number of samples: 3 -62: Average distance: 1.72076 nm -62: Standard deviation: 1.24839 nm -62: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) -62: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: Contacts: -62: Number of samples: 2 -62: Average distance: 1.00000 nm -62: Standard deviation: 0.00000 nm -62: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) -62: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: SuccessiveContacts: -62: Number of samples: 2 -62: Average distance: 1.00000 nm -62: Standard deviation: 0.00000 nm -62: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) -62: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: ManyContacts: -62: Number of samples: 10 -62: Average distance: 1.82913 nm -62: Standard deviation: 0.78478 nm -62: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) -62: [----------] 6 tests from DistanceModuleTest (17 ms total) -62: -62: [----------] 2 tests from ExtractClusterModuleTest -62: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms -62: trr version: GMX_trn_file (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -62: Analyzed 26 frames, last time 0.050 -62: There are 8 clusters containing 26 structures, highest framenr is 25 -62: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (5 ms) -62: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset -62: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 -62: Analyzed 26 frames, last time 0.050 -62: There are 8 clusters containing 26 structures, highest framenr is 25 -62: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (9 ms) -62: [----------] 2 tests from ExtractClusterModuleTest (14 ms total) -62: -62: [----------] 2 tests from FreeVolumeModuleTest -62: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for CO2-RM. Set to zero. -62: Could not determine VDW radius for 40 particles. These were set to zero. -62: Reading frame 0 time 0.000 Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: cutoff = 0.18 nm -62: probe_radius = 0 nm -62: seed = 13 -62: ninsert = 1000 probes per nm^3 -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -62: Spoel, Luciano T. Costa -62: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -62: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -62: Environ. Sci. Technol. (2013) -62: DOI: 10.1021/es4020986 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Free volume 38.02 +/- 0.00 % -62: Total volume 68.92 +/- 0.00 nm^3 -62: Number of molecules 340 total mass 63491.38 Dalton -62: Average molar mass: 186.74 Dalton -62: Density rho: 1529.71 +/- 0.00 nm^3 -62: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -62: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 -62: Fractional free volume 0.194 +/- 0.000 -62: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (49 ms) -62: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Reading frame 0 time 0.000 Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: cutoff = 0.18 nm -62: probe_radius = 0 nm -62: seed = 17 -62: ninsert = 1000 probes per nm^3 -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der -62: Spoel, Luciano T. Costa -62: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium -62: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View -62: Environ. Sci. Technol. (2013) -62: DOI: 10.1021/es4020986 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Free volume 38.48 +/- 0.00 % -62: Total volume 68.92 +/- 0.00 nm^3 -62: Number of molecules 340 total mass 63491.38 Dalton -62: Average molar mass: 186.74 Dalton -62: Density rho: 1529.71 +/- 0.00 nm^3 -62: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 -62: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 -62: Fractional free volume 0.200 +/- 0.000 -62: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (49 ms) -62: [----------] 2 tests from FreeVolumeModuleTest (98 ms total) -62: -62: [----------] 13 tests from MsdModuleTest -62: [ RUN ] MsdModuleTest.threeDimensionalDiffusion -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -62: Analyzed 10 frames, last time 9.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] MsdModuleTest.threeDimensionalDiffusion (2 ms) -62: [ RUN ] MsdModuleTest.twoDimensionalDiffusion -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -62: Analyzed 10 frames, last time 9.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) -62: [ RUN ] MsdModuleTest.oneDimensionalDiffusion -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -62: Analyzed 10 frames, last time 9.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) -62: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau -62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 -62: Analyzed 10 frames, last time 9.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) -62: [ RUN ] MsdModuleTest.multipleGroupsWork -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to 2046797695 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.multipleGroupsWork (17 ms) -62: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 0.100 -62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -62: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 -62: Analyzed 21 frames, last time 2.000 -62: Setting the LD random seed to -16801795 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (16 ms) -62: [ RUN ] MsdModuleTest.trestartLessThanDt -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -17891351 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.trestartLessThanDt (12 ms) -62: [ RUN ] MsdModuleTest.trestartGreaterThanDt -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to -16769 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.trestartGreaterThanDt (15 ms) -62: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -270549025 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (11 ms) -62: [ RUN ] MsdModuleTest.molTest -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to -545262415 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.molTest (15 ms) -62: [ RUN ] MsdModuleTest.beginFit -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to 1073206143 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.beginFit (15 ms) -62: [ RUN ] MsdModuleTest.endFit -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to 1593044662 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.endFit (15 ms) -62: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: -62: For energy conservation with LINCS, lincs_iter should be 2 or larger. -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 1818.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -62: NVE simulation: will use the initial temperature of 288.764 K for -62: determining the Verlet buffer size -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -62: There are 9 non-linear virtual site constructions. Their contribution to -62: the energy error is approximated. In most cases this does not affect the -62: error significantly. -62: -62: -62: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 5 NOTEs -62: NOTE: You provided an index file -62: /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx -62: (with -n), but it was not used by any selection. -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 -62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. -62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 -62: Analyzed 21 frames, last time 40.000 -62: Setting the LD random seed to -1176620402 -62: -62: Generated 2145 of the 2145 non-bonded parameter combinations -62: -62: Generated 2145 of the 2145 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -62: -62: Excluding 2 bonded neighbours molecule type 'SOL' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' -62: -62: Cleaning up constraints and constant bonded interactions with virtual sites -62: -62: Converted 15 Bonds with virtual sites to connections, 7 left -62: -62: Removed 18 Angles with virtual sites, 21 left -62: -62: Removed 10 Proper Dih.s with virtual sites, 44 left -62: -62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K -62: -62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm -62: -62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm -62: -62: Note that mdrun will redetermine rlist based on the actual pair-list setup -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (16 ms) -62: [----------] 13 tests from MsdModuleTest (143 ms total) -62: -62: [----------] 9 tests from PairDistanceModuleTest -62: [ RUN ] PairDistanceModuleTest.ComputesAllDistances -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) -62: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) -62: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) -62: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) -62: [----------] 9 tests from PairDistanceModuleTest (13 ms total) -62: -62: [----------] 5 tests from RdfModuleTest -62: [ RUN ] RdfModuleTest.BasicTest -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] RdfModuleTest.BasicTest (12 ms) -62: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork -62: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. -62: Reading frame 0 time 0.000 Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (10 ms) -62: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (12 ms) -62: [ RUN ] RdfModuleTest.CalculatesSurf -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) -62: [ RUN ] RdfModuleTest.CalculatesXY -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] RdfModuleTest.CalculatesXY (13 ms) -62: [----------] 5 tests from RdfModuleTest (53 ms total) -62: -62: [----------] 5 tests from SasaModuleTest -62: [ RUN ] SasaModuleTest.BasicTest -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -62: of Surface Area and Volume and to Dot Surface Contouring of Molecular -62: Assemblies -62: J. Comp. Chem. (1995) -62: DOI: 10.1002/jcc.540160303 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Analyzed topology coordinates -62: [ OK ] SasaModuleTest.BasicTest (5 ms) -62: [ RUN ] SasaModuleTest.HandlesSelectedResidues -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -62: of Surface Area and Volume and to Dot Surface Contouring of Molecular -62: Assemblies -62: J. Comp. Chem. (1995) -62: DOI: 10.1002/jcc.540160303 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Analyzed topology coordinates -62: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) -62: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -62: of Surface Area and Volume and to Dot Surface Contouring of Molecular -62: Assemblies -62: J. Comp. Chem. (1995) -62: DOI: 10.1002/jcc.540160303 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Analyzed topology coordinates -62: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (3 ms) -62: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -62: of Surface Area and Volume and to Dot Surface Contouring of Molecular -62: Assemblies -62: J. Comp. Chem. (1995) -62: DOI: 10.1002/jcc.540160303 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Analyzed topology coordinates -62: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) -62: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf -62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration -62: of Surface Area and Volume and to Dot Surface Contouring of Molecular -62: Assemblies -62: J. Comp. Chem. (1995) -62: DOI: 10.1002/jcc.540160303 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii -62: from the source below. This means the results may be different -62: compared to previous GROMACS versions. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. Bondi -62: van der Waals Volumes and Radii -62: J. Phys. Chem. (1964) -62: DOI: 10.1021/j100785a001 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Analyzed topology coordinates -62: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (4 ms) -62: [----------] 5 tests from SasaModuleTest (23 ms total) -62: -62: [----------] 8 tests from SelectModuleTest -62: [ RUN ] SelectModuleTest.BasicTest -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.BasicTest (3 ms) -62: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) -62: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) -62: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) -62: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) -62: [ RUN ] SelectModuleTest.NormalizesSizes -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) -62: [ RUN ] SelectModuleTest.WritesResidueNumbers -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) -62: [ RUN ] SelectModuleTest.WritesResidueIndices -62: Analyzed topology coordinates -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) -62: [----------] 8 tests from SelectModuleTest (14 ms total) -62: -62: [----------] 10 tests from SurfaceAreaTest -62: [ RUN ] SurfaceAreaTest.ComputesSinglePoint -62: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) -62: [ RUN ] SurfaceAreaTest.ComputesTwoPoints -62: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) -62: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius -62: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) -62: [ RUN ] SurfaceAreaTest.SurfacePoints12 -62: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) -62: [ RUN ] SurfaceAreaTest.SurfacePoints32 -62: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) -62: [ RUN ] SurfaceAreaTest.SurfacePoints42 -62: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) -62: [ RUN ] SurfaceAreaTest.SurfacePoints122 -62: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) -62: [ RUN ] SurfaceAreaTest.Computes100Points -62: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) -62: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC -62: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) -62: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC -62: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) -62: [----------] 10 tests from SurfaceAreaTest (6 ms total) -62: -62: [----------] 4 tests from TopologyInformation -62: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile -62: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) -62: [ RUN ] TopologyInformation.WorksWithGroFile -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) -62: [ RUN ] TopologyInformation.WorksWithPdbFile -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) -62: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile -62: -62: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -62: For a correct single-point energy evaluation with nsteps = 0, use -62: continuation = yes to avoid constraining the input coordinates. -62: -62: Generating 1-4 interactions: fudge = 0.5 -62: -62: NOTE 2 [file lysozyme.top, line 1465]: -62: System has non-zero total charge: 2.000000 -62: Total charge should normally be an integer. See -62: https://manual.gromacs.org/current/user-guide/floating-point.html -62: for discussion on how close it should be to an integer. -62: -62: -62: -62: Number of degrees of freedom in T-Coupling group rest is 465.00 -62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -62: -62: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -62: NVE simulation with an initial temperature of zero: will use a Verlet -62: buffer of 10%. Check your energy drift! -62: -62: -62: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: -62: You are using a plain Coulomb cut-off, which might produce artifacts. -62: You might want to consider using PME electrostatics. -62: -62: -62: -62: There were 4 NOTEs -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -62: Setting the LD random seed to -1074962954 -62: -62: Generated 330891 of the 330891 non-bonded parameter combinations -62: -62: Generated 330891 of the 330891 1-4 parameter combinations -62: -62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -62: -62: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -62: Analysing residue names: -62: There are: 10 Protein residues -62: Analysing Protein... -62: -62: This run will generate roughly 0 Mb of data -62: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (234 ms) -62: [----------] 4 tests from TopologyInformation (237 ms total) -62: -62: [----------] 4 tests from TrajectoryModuleTest -62: [ RUN ] TrajectoryModuleTest.BasicTest -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) -62: [ RUN ] TrajectoryModuleTest.PlotsXOnly -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) -62: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) -62: [ RUN ] TrajectoryModuleTest.HandlesNoForces -62: Reading frames from gro file 'Test system', 15 atoms. -62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 -62: Analyzed 2 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) -62: [----------] 4 tests from TrajectoryModuleTest (7 ms total) -62: -62: [----------] 5 tests from UnionFinderTest -62: [ RUN ] UnionFinderTest.WorksEmpty -62: [ OK ] UnionFinderTest.WorksEmpty (0 ms) -62: [ RUN ] UnionFinderTest.BasicMerges -62: [ OK ] UnionFinderTest.BasicMerges (0 ms) -62: [ RUN ] UnionFinderTest.LargerMerges -62: [ OK ] UnionFinderTest.LargerMerges (0 ms) -62: [ RUN ] UnionFinderTest.LongRightMerge -62: [ OK ] UnionFinderTest.LongRightMerge (0 ms) -62: [ RUN ] UnionFinderTest.LongLeftMerge -62: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) -62: [----------] 5 tests from UnionFinderTest (0 ms total) -62: -62: [----------] 1 test from MappedUnionFinderTest -62: [ RUN ] MappedUnionFinderTest.BasicMerges -62: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) -62: [----------] 1 test from MappedUnionFinderTest (0 ms total) -62: -62: [----------] 192 tests from MoleculeTests/DsspModuleTest -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (15 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (14 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (12 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (11 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (11 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (13 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (9 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (10 ms) -62: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 -62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms -62: Last frame 0 time 500.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: W. Kabsch, C. Sander -62: Dictionary of protein secondary structure: pattern recognition of -62: hydrogen-bonded and geometrical features -62: Biopolymers (1983) -62: DOI: 10.1002/bip.360221211 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in -62: Trajectories -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c01344 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (10 ms) -62: [----------] 192 tests from MoleculeTests/DsspModuleTest (2412 ms total) -62: -62: [----------] 3 tests from GyrateTests/GyrateModuleTest -62: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (5 ms) -62: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) -62: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) -62: [----------] 3 tests from GyrateTests/GyrateModuleTest (13 ms total) -62: -62: [----------] 96 tests from HBondTests/HbondModuleTest -62: [ RUN ] HBondTests/HbondModuleTest.Works/0 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/0 (9 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/1 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/1 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/2 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/2 (6 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/3 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/3 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/4 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/4 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/5 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/5 (8 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/6 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/6 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/7 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/7 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/8 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/8 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/9 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/9 (8 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/10 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/10 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/11 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/11 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/12 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/12 (9 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/13 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/13 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/14 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/14 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/15 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/15 (6 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/16 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/16 (10 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/17 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/17 (9 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/18 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/18 (8 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/19 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/19 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/20 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/20 (8 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/21 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/21 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/22 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/22 (6 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/23 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/23 (6 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/24 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/24 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/25 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/25 (8 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/26 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/26 (6 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/27 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/27 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/28 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/28 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/29 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/29 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/30 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/30 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/31 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/31 (7 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/32 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/32 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/33 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/33 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/34 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/34 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/35 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/35 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/36 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/36 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/37 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/37 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/38 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/38 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/39 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/39 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/40 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/40 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/41 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/41 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/42 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/42 (104 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/43 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/43 (38 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/44 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/44 (39 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/45 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/45 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/46 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/46 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/47 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/47 (63 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/48 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/48 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/49 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/49 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/50 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/50 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/51 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/51 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/52 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/52 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/53 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/53 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/54 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/54 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/55 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/55 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/56 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/56 (39 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/57 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/57 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/58 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/58 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/59 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/59 (32 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/60 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/60 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/61 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 27 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/61 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/62 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 56 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/62 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/63 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) -62: Selection 'Protein' has 29 acceptors and 4 donors. -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: Merging hbonds with Acceptor and Donor swapped -62: [ OK ] HBondTests/HbondModuleTest.Works/63 (31 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/64 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/64 (38 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/65 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/65 (33 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/66 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/66 (57 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/67 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/67 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/68 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/68 (39 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/69 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/69 (39 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/70 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/70 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/71 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/71 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/72 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/72 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/73 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/73 (39 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/74 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/74 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/75 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/75 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/76 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/76 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/77 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/77 (38 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/78 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/78 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/79 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/79 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/80 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/80 (40 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/81 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/81 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/82 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/82 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/83 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/83 (34 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/84 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/84 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/85 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/85 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/86 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/86 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/87 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/87 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/88 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/88 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/89 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/89 (37 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/90 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/90 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/91 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/91 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/92 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/92 (35 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/93 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/93 (38 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/94 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/94 (36 ms) -62: [ RUN ] HBondTests/HbondModuleTest.Works/95 -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) -62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 -62: Analyzed 2 frames, last time 10.000 -62: -62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) -62: Selection 'Water' has 1160 acceptors and 1160 donors. -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov -62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome -62: Memory Limitation -62: Journal of Chemical Information and Modeling (2024) -62: DOI: 10.1021/acs.jcim.3c02087 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] HBondTests/HbondModuleTest.Works/95 (36 ms) -62: [----------] 96 tests from HBondTests/HbondModuleTest (2971 ms total) -62: -62: [----------] 4 tests from MoleculeTests/ScatteringModule -62: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -62: Method for calculating small-angle neutron scattering spectra using all-atom -62: molecular dynamics trajectories -62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -62: DOI: 10.1134/S1027451013060372 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) -62: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -62: Method for calculating small-angle neutron scattering spectra using all-atom -62: molecular dynamics trajectories -62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -62: DOI: 10.1134/S1027451013060372 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: D. T. Cromer, J. B. Mann -62: X-ray scattering factors computed from numerical Hartree-Fock wave functions -62: Acta Cryst. A (1968) -62: DOI: 10.1107/S0567739468000550 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (187 ms) -62: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -62: Method for calculating small-angle neutron scattering spectra using all-atom -62: molecular dynamics trajectories -62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -62: DOI: 10.1134/S1027451013060372 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) -62: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 -62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms -62: Last frame 0 time 0.000 -62: Analyzed 1 frames, last time 0.000 -62: -62: WARNING: Masses and atomic (Van der Waals) radii will be guessed -62: based on residue and atom names, since they could not be -62: definitively assigned from the information in your input -62: files. These guessed numbers might deviate from the mass -62: and radius of the atom type. Please check the output -62: files if necessary. Note, that this functionality may -62: be removed in a future GROMACS version. Please, consider -62: using another file format for your input. -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov -62: Method for calculating small-angle neutron scattering spectra using all-atom -62: molecular dynamics trajectories -62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) -62: DOI: 10.1134/S1027451013060372 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: -62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -62: D. T. Cromer, J. B. Mann -62: X-ray scattering factors computed from numerical Hartree-Fock wave functions -62: Acta Cryst. A (1968) -62: DOI: 10.1107/S0567739468000550 -62: -------- -------- --- Thank You --- -------- -------- -62: -62: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (43 ms) -62: [----------] 4 tests from MoleculeTests/ScatteringModule (244 ms total) -62: -62: [----------] Global test environment tear-down -62: [==========] 393 tests from 21 test suites ran. (6321 ms total) -62: [ PASSED ] 393 tests. -62/96 Test #62: TrajectoryAnalysisUnitTests .................. Passed 6.52 sec -test 63 - Start 63: EnergyAnalysisUnitTests - -63: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" -63: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/energyanalysis/tests -63: Test timeout computed to be: 30 -63: [==========] Running 12 tests from 5 test suites. -63: [----------] Global test environment set-up. -63: [----------] 2 tests from EnergyTermTest -63: [ RUN ] EnergyTermTest.ConstructWorks -63: [ OK ] EnergyTermTest.ConstructWorks (0 ms) -63: [ RUN ] EnergyTermTest.AddFrameWorks -63: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) -63: [----------] 2 tests from EnergyTermTest (0 ms total) -63: -63: [----------] 1 test from DhdlTest -63: [ RUN ] DhdlTest.ExtractDhdl -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file -63: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) -63: Note: file tpx version 110, software tpx version 137 -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 -63: -63: -63: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg -63: [ OK ] DhdlTest.ExtractDhdl (6 ms) -63: [----------] 1 test from DhdlTest (6 ms total) -63: -63: [----------] 1 test from OriresTest -63: [ RUN ] OriresTest.ExtractOrires -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file -63: Reading file /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) -63: Note: file tpx version 111, software tpx version 137 -63: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) -63: End your selection with 0 -63: Selecting all 7 orientation restraints -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 -63: [ OK ] OriresTest.ExtractOrires (7 ms) -63: [----------] 1 test from OriresTest (7 ms total) -63: -63: [----------] 5 tests from EnergyTest -63: [ RUN ] EnergyTest.ExtractEnergy -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: -63: Select the terms you want from the following list by -63: selecting either (part of) the name or the number or a combination. -63: End your selection with an empty line or a zero. -63: ------------------------------------------------------------------- -63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -63: 13 Box-Z 14 Volume 15 Density 16 pV -63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -63: -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) -63: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -63: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -63: [ OK ] EnergyTest.ExtractEnergy (2 ms) -63: [ RUN ] EnergyTest.ExtractEnergyByNumber -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: -63: Select the terms you want from the following list by -63: selecting either (part of) the name or the number or a combination. -63: End your selection with an empty line or a zero. -63: ------------------------------------------------------------------- -63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -63: 13 Box-Z 14 Volume 15 Density 16 pV -63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -63: -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) -63: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) -63: Pres. DC -268.49 3 8.52175 13.2804 (bar) -63: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) -63: [ RUN ] EnergyTest.ExtractEnergyMixed -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: -63: Select the terms you want from the following list by -63: selecting either (part of) the name or the number or a combination. -63: End your selection with an empty line or a zero. -63: ------------------------------------------------------------------- -63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. -63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature -63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y -63: 13 Box-Z 14 Volume 15 Density 16 pV -63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ -63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX -63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY -63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ -63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen -63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System -63: -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) -63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -63: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) -63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -63: [ OK ] EnergyTest.ExtractEnergyMixed (2 ms) -63: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -63: -63: Select the terms you want from the following list by -63: selecting either (part of) the name or the number or a combination. -63: End your selection with an empty line or a zero. -63: ------------------------------------------------------------------- -63: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -63: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -63: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -63: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -63: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -63: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -63: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -63: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -63: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -63: 37 1/Viscosity 38 T-System 39 Lamb-System -63: -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -63: -63: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets -63: All statistics are over 3 points (frames) -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -63: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) -63: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file -63: -63: Select the terms you want from the following list by -63: selecting either (part of) the name or the number or a combination. -63: End your selection with an empty line or a zero. -63: ------------------------------------------------------------------- -63: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. -63: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) -63: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy -63: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd -63: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX -63: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY -63: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ -63: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX -63: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X -63: 37 1/Viscosity 38 T-System 39 Lamb-System -63: -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 -63: -63: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets -63: All statistics are over 3 points (frames) -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) -63: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) -63: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) -63: [----------] 5 tests from EnergyTest (8 ms total) -63: -63: [----------] 3 tests from ViscosityTest -63: [ RUN ] ViscosityTest.EinsteinViscosity -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Pres-XX 20.2092 65 717.193 185.978 (bar) -63: Pres-XY -47.7351 39 372.522 207.456 (bar) -63: Pres-XZ 11.477 31 379.79 6.80818 (bar) -63: Pres-YX -47.7106 39 372.525 207.5 (bar) -63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -63: Pres-YZ -41.3534 45 401.216 114.663 (bar) -63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -63: Pres-ZY -41.3119 45 401.196 114.743 (bar) -63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -63: -63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -63: [ OK ] ViscosityTest.EinsteinViscosity (42 ms) -63: [ RUN ] ViscosityTest.EinsteinViscosityIntegral -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Pres-XX 20.2092 65 717.193 185.978 (bar) -63: Pres-XY -47.7351 39 372.522 207.456 (bar) -63: Pres-XZ 11.477 31 379.79 6.80818 (bar) -63: Pres-YX -47.7106 39 372.525 207.5 (bar) -63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -63: Pres-YZ -41.3534 45 401.216 114.663 (bar) -63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -63: Pres-ZY -41.3119 45 401.196 114.743 (bar) -63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -63: -63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -63: [ OK ] ViscosityTest.EinsteinViscosityIntegral (35 ms) -63: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments -63: Opened /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file -63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 -63: -63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets -63: All statistics are over 5001 points -63: -63: Energy Average Err.Est. RMSD Tot-Drift -63: ------------------------------------------------------------------------------- -63: Pres-XX 20.2092 65 717.193 185.978 (bar) -63: Pres-XY -47.7351 39 372.522 207.456 (bar) -63: Pres-XZ 11.477 31 379.79 6.80818 (bar) -63: Pres-YX -47.7106 39 372.525 207.5 (bar) -63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) -63: Pres-YZ -41.3534 45 401.216 114.663 (bar) -63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) -63: Pres-ZY -41.3119 45 401.196 114.743 (bar) -63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) -63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) -63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) -63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) -63: -63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps -63: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (36 ms) -63: [----------] 3 tests from ViscosityTest (114 ms total) -63: -63: [----------] Global test environment tear-down -63: [==========] 12 tests from 5 test suites ran. (137 ms total) -63: [ PASSED ] 12 tests. -63/96 Test #63: EnergyAnalysisUnitTests ...................... Passed 0.33 sec -test 64 - Start 64: ToolUnitTests - -64: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/ToolUnitTests.xml" -64: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests -64: Test timeout computed to be: 1920 -64: [==========] Running 63 tests from 8 test suites. -64: [----------] Global test environment set-up. -64: [----------] 2 tests from DumpTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Setting the LD random seed to -1209151489 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: [ RUN ] DumpTest.WorksWithTpr -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: -64: inputrec: -64: integrator = md -64: tinit = 0 -64: dt = 0.001 -64: nsteps = 0 -64: init-step = 0 -64: simulation-part = 1 -64: mts = false -64: mass-repartition-factor = 1 -64: comm-mode = Linear -64: nstcomm = 100 -64: bd-fric = 0 -64: ld-seed = -1209151489 -64: emtol = 10 -64: emstep = 0.01 -64: niter = 20 -64: fcstep = 0 -64: nstcgsteep = 1000 -64: nbfgscorr = 10 -64: rtpi = 0.05 -64: nstxout = 0 -64: nstvout = 0 -64: nstfout = 0 -64: nstlog = 1000 -64: nstcalcenergy = 100 -64: nstenergy = 1000 -64: nstxout-compressed = 0 -64: compressed-x-precision = 1000 -64: cutoff-scheme = Verlet -64: nstlist = 10 -64: pbc = xyz -64: periodic-molecules = false -64: verlet-buffer-tolerance = -1 -64: verlet-buffer-pressure-tolerance = 0.5 -64: rlist = 1.1 -64: coulombtype = Cut-off -64: coulomb-modifier = Potential-shift -64: rcoulomb-switch = 0 -64: rcoulomb = 1 -64: epsilon-r = 1 -64: epsilon-rf = inf -64: vdw-type = Cut-off -64: vdw-modifier = Potential-shift -64: rvdw-switch = 0 -64: rvdw = 1 -64: DispCorr = No -64: table-extension = 1 -64: fourierspacing = 0.12 -64: fourier-nx = 0 -64: fourier-ny = 0 -64: fourier-nz = 0 -64: pme-order = 4 -64: ewald-rtol = 1e-05 -64: ewald-rtol-lj = 0.001 -64: lj-pme-comb-rule = Geometric -64: ewald-geometry = 3d -64: epsilon-surface = 0 -64: ensemble-temperature-setting = not available -64: tcoupl = No -64: nsttcouple = -1 -64: nh-chain-length = 0 -64: print-nose-hoover-chain-variables = false -64: pcoupl = No -64: refcoord-scaling = No -64: posres-com: not available -64: posres-comB: not available -64: QMMM = false -64: qm-opts: -64: ngQM = 0 -64: constraint-algorithm = Lincs -64: continuation = false -64: Shake-SOR = false -64: shake-tol = 0.0001 -64: lincs-order = 4 -64: lincs-iter = 1 -64: lincs-warnangle = 30 -64: nwall = 0 -64: wall-type = 9-3 -64: wall-r-linpot = -1 -64: wall-atomtype[0] = -1 -64: wall-atomtype[1] = -1 -64: wall-density[0] = 0 -64: wall-density[1] = 0 -64: wall-ewald-zfac = 3 -64: pull = false -64: awh = false -64: rotation = false -64: interactiveMD = false -64: disre = No -64: disre-weighting = Conservative -64: disre-mixed = false -64: dr-fc = 1000 -64: dr-tau = 0 -64: nstdisreout = 100 -64: orire-fc = 0 -64: orire-tau = 0 -64: nstorireout = 100 -64: free-energy = no -64: cos-acceleration = 0 -64: deform (3x3): -64: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: simulated-tempering = false -64: swapcoords = no -64: userint1 = 0 -64: userint2 = 0 -64: userint3 = 0 -64: userint4 = 0 -64: userreal1 = 0 -64: userreal2 = 0 -64: userreal3 = 0 -64: userreal4 = 0 -64: applied-forces: -64: electric-field: -64: x: -64: E0 = 0 -64: omega = 0 -64: t0 = 0 -64: sigma = 0 -64: y: -64: E0 = 0 -64: omega = 0 -64: t0 = 0 -64: sigma = 0 -64: z: -64: E0 = 0 -64: omega = 0 -64: t0 = 0 -64: sigma = 0 -64: density-guided-simulation: -64: active = false -64: group = protein -64: similarity-measure = inner-product -64: atom-spreading-weight = unity -64: force-constant = 1e+09 -64: gaussian-transform-spreading-width = 0.2 -64: gaussian-transform-spreading-range-in-multiples-of-width = 4 -64: reference-density-filename = reference.mrc -64: nst = 1 -64: normalize-densities = true -64: adaptive-force-scaling = false -64: adaptive-force-scaling-time-constant = 4 -64: shift-vector = -64: transformation-matrix = -64: qmmm-cp2k: -64: active = false -64: qmgroup = System -64: qmmethod = PBE -64: qmfilenames = -64: qmcharge = 0 -64: qmmultiplicity = 1 -64: colvars: -64: active = false -64: configfile = -64: seed = -1 -64: nnpot: -64: active = false -64: modelfile = model.pt -64: input-group = System -64: model-input1 = -64: model-input2 = -64: model-input3 = -64: model-input4 = -64: grpopts: -64: nrdf: 465 -64: ref-t: 0 -64: tau-t: 0 -64: annealing: No -64: annealing-npoints: 0 -64: acc: 0 0 0 -64: nfreeze: N N N -64: energygrp-flags[ 0]: 0 -64: header: -64: bIr = present -64: bBox = present -64: bTop = present -64: bX = present -64: bV = present -64: bF = not present -64: natoms = 156 -64: lambda = 0.000000e+00 -64: buffer size = 46382 -64: topology: -64: name="First 10 residues from 1AKI" -64: #atoms = 156 -64: #molblock = 1 -64: molblock (0): -64: moltype = 0 "Protein_chain_B" -64: #molecules = 1 -64: #posres_xA = 0 -64: #posres_xB = 0 -64: bIntermolecularInteractions = false -64: ffparams: -64: atnr=10 -64: ntypes=212 -64: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 -64: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 -64: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 -64: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 -64: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 -64: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 -64: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 -64: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 -64: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 -64: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 -64: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 -64: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 -64: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 -64: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 -64: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 -64: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 -64: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 -64: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 -64: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 -64: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 -64: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 -64: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 -64: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 -64: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 -64: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 -64: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 -64: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 -64: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 -64: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 -64: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 -64: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 -64: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 -64: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 -64: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 -64: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 -64: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 -64: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 -64: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 -64: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 -64: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 -64: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 -64: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 -64: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 -64: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 -64: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 -64: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 -64: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 -64: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 -64: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 -64: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 -64: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 -64: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 -64: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 -64: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 -64: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 -64: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 -64: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 -64: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 -64: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 -64: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 -64: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 -64: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 -64: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 -64: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 -64: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 -64: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 -64: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 -64: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 -64: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 -64: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 -64: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 -64: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 -64: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 -64: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 -64: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 -64: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 -64: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 -64: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 -64: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 -64: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 -64: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 -64: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 -64: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 -64: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 -64: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 -64: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 -64: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 -64: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 -64: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 -64: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 -64: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 -64: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 -64: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 -64: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 -64: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 -64: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 -64: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 -64: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 -64: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 -64: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 -64: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 -64: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 -64: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 -64: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 -64: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 -64: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 -64: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 -64: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 -64: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 -64: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 -64: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 -64: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 -64: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 -64: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 -64: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 -64: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 -64: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 -64: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 -64: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 -64: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 -64: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 -64: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 -64: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 -64: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 -64: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 -64: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 -64: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 -64: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 -64: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 -64: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 -64: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 -64: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 -64: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 -64: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 -64: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 -64: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 -64: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 -64: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 -64: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 -64: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 -64: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 -64: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 -64: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 -64: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 -64: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 -64: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 -64: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 -64: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 -64: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 -64: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 -64: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 -64: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 -64: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 -64: reppow = 12 -64: fudgeQQ = 0.5 -64: cmap -64: moltype (0): -64: name="Protein_chain_B" -64: atoms: -64: atom (156): -64: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -64: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} -64: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -64: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -64: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} -64: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} -64: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} -64: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} -64: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} -64: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} -64: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} -64: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} -64: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} -64: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} -64: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} -64: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -64: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} -64: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} -64: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} -64: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} -64: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} -64: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} -64: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} -64: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -64: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} -64: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -64: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} -64: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -64: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -64: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -64: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -64: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} -64: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} -64: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} -64: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} -64: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} -64: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} -64: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} -64: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -64: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} -64: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} -64: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} -64: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} -64: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} -64: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} -64: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} -64: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} -64: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} -64: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} -64: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} -64: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} -64: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} -64: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -64: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -64: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -64: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} -64: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -64: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} -64: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} -64: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} -64: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} -64: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} -64: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} -64: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -64: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} -64: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -64: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} -64: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} -64: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} -64: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} -64: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} -64: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} -64: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} -64: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} -64: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -64: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} -64: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -64: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -64: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} -64: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -64: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} -64: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} -64: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -64: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} -64: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} -64: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} -64: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} -64: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} -64: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} -64: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} -64: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} -64: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -64: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} -64: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} -64: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} -64: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} -64: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} -64: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} -64: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} -64: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -64: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} -64: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -64: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -64: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} -64: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} -64: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} -64: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} -64: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} -64: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} -64: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -64: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} -64: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -64: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -64: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} -64: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} -64: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} -64: atom (156): -64: atom[0]={name="N"} -64: atom[1]={name="H1"} -64: atom[2]={name="H2"} -64: atom[3]={name="H3"} -64: atom[4]={name="CA"} -64: atom[5]={name="HA"} -64: atom[6]={name="CB"} -64: atom[7]={name="HB1"} -64: atom[8]={name="HB2"} -64: atom[9]={name="CG"} -64: atom[10]={name="HG1"} -64: atom[11]={name="HG2"} -64: atom[12]={name="CD"} -64: atom[13]={name="HD1"} -64: atom[14]={name="HD2"} -64: atom[15]={name="CE"} -64: atom[16]={name="HE1"} -64: atom[17]={name="HE2"} -64: atom[18]={name="NZ"} -64: atom[19]={name="HZ1"} -64: atom[20]={name="HZ2"} -64: atom[21]={name="HZ3"} -64: atom[22]={name="C"} -64: atom[23]={name="O"} -64: atom[24]={name="N"} -64: atom[25]={name="H"} -64: atom[26]={name="CA"} -64: atom[27]={name="HA"} -64: atom[28]={name="CB"} -64: atom[29]={name="HB"} -64: atom[30]={name="CG1"} -64: atom[31]={name="HG11"} -64: atom[32]={name="HG12"} -64: atom[33]={name="HG13"} -64: atom[34]={name="CG2"} -64: atom[35]={name="HG21"} -64: atom[36]={name="HG22"} -64: atom[37]={name="HG23"} -64: atom[38]={name="C"} -64: atom[39]={name="O"} -64: atom[40]={name="N"} -64: atom[41]={name="H"} -64: atom[42]={name="CA"} -64: atom[43]={name="HA"} -64: atom[44]={name="CB"} -64: atom[45]={name="HB1"} -64: atom[46]={name="HB2"} -64: atom[47]={name="CG"} -64: atom[48]={name="CD1"} -64: atom[49]={name="HD1"} -64: atom[50]={name="CD2"} -64: atom[51]={name="HD2"} -64: atom[52]={name="CE1"} -64: atom[53]={name="HE1"} -64: atom[54]={name="CE2"} -64: atom[55]={name="HE2"} -64: atom[56]={name="CZ"} -64: atom[57]={name="HZ"} -64: atom[58]={name="C"} -64: atom[59]={name="O"} -64: atom[60]={name="N"} -64: atom[61]={name="H"} -64: atom[62]={name="CA"} -64: atom[63]={name="HA1"} -64: atom[64]={name="HA2"} -64: atom[65]={name="C"} -64: atom[66]={name="O"} -64: atom[67]={name="N"} -64: atom[68]={name="H"} -64: atom[69]={name="CA"} -64: atom[70]={name="HA"} -64: atom[71]={name="CB"} -64: atom[72]={name="HB1"} -64: atom[73]={name="HB2"} -64: atom[74]={name="CG"} -64: atom[75]={name="HG1"} -64: atom[76]={name="HG2"} -64: atom[77]={name="CD"} -64: atom[78]={name="HD1"} -64: atom[79]={name="HD2"} -64: atom[80]={name="NE"} -64: atom[81]={name="HE"} -64: atom[82]={name="CZ"} -64: atom[83]={name="NH1"} -64: atom[84]={name="HH11"} -64: atom[85]={name="HH12"} -64: atom[86]={name="NH2"} -64: atom[87]={name="HH21"} -64: atom[88]={name="HH22"} -64: atom[89]={name="C"} -64: atom[90]={name="O"} -64: atom[91]={name="N"} -64: atom[92]={name="H"} -64: atom[93]={name="CA"} -64: atom[94]={name="HA"} -64: atom[95]={name="CB"} -64: atom[96]={name="HB1"} -64: atom[97]={name="HB2"} -64: atom[98]={name="SG"} -64: atom[99]={name="HG"} -64: atom[100]={name="C"} -64: atom[101]={name="O"} -64: atom[102]={name="N"} -64: atom[103]={name="H"} -64: atom[104]={name="CA"} -64: atom[105]={name="HA"} -64: atom[106]={name="CB"} -64: atom[107]={name="HB1"} -64: atom[108]={name="HB2"} -64: atom[109]={name="CG"} -64: atom[110]={name="HG1"} -64: atom[111]={name="HG2"} -64: atom[112]={name="CD"} -64: atom[113]={name="OE1"} -64: atom[114]={name="OE2"} -64: atom[115]={name="C"} -64: atom[116]={name="O"} -64: atom[117]={name="N"} -64: atom[118]={name="H"} -64: atom[119]={name="CA"} -64: atom[120]={name="HA"} -64: atom[121]={name="CB"} -64: atom[122]={name="HB1"} -64: atom[123]={name="HB2"} -64: atom[124]={name="CG"} -64: atom[125]={name="HG"} -64: atom[126]={name="CD1"} -64: atom[127]={name="HD11"} -64: atom[128]={name="HD12"} -64: atom[129]={name="HD13"} -64: atom[130]={name="CD2"} -64: atom[131]={name="HD21"} -64: atom[132]={name="HD22"} -64: atom[133]={name="HD23"} -64: atom[134]={name="C"} -64: atom[135]={name="O"} -64: atom[136]={name="N"} -64: atom[137]={name="H"} -64: atom[138]={name="CA"} -64: atom[139]={name="HA"} -64: atom[140]={name="CB"} -64: atom[141]={name="HB1"} -64: atom[142]={name="HB2"} -64: atom[143]={name="HB3"} -64: atom[144]={name="C"} -64: atom[145]={name="O"} -64: atom[146]={name="N"} -64: atom[147]={name="H"} -64: atom[148]={name="CA"} -64: atom[149]={name="HA"} -64: atom[150]={name="CB"} -64: atom[151]={name="HB1"} -64: atom[152]={name="HB2"} -64: atom[153]={name="HB3"} -64: atom[154]={name="C"} -64: atom[155]={name="O"} -64: type (156): -64: type[0]={name="opls_287",nameB="opls_287"} -64: type[1]={name="opls_290",nameB="opls_290"} -64: type[2]={name="opls_290",nameB="opls_290"} -64: type[3]={name="opls_290",nameB="opls_290"} -64: type[4]={name="opls_293B",nameB="opls_293B"} -64: type[5]={name="opls_140",nameB="opls_140"} -64: type[6]={name="opls_136",nameB="opls_136"} -64: type[7]={name="opls_140",nameB="opls_140"} -64: type[8]={name="opls_140",nameB="opls_140"} -64: type[9]={name="opls_136",nameB="opls_136"} -64: type[10]={name="opls_140",nameB="opls_140"} -64: type[11]={name="opls_140",nameB="opls_140"} -64: type[12]={name="opls_136",nameB="opls_136"} -64: type[13]={name="opls_140",nameB="opls_140"} -64: type[14]={name="opls_140",nameB="opls_140"} -64: type[15]={name="opls_292",nameB="opls_292"} -64: type[16]={name="opls_140",nameB="opls_140"} -64: type[17]={name="opls_140",nameB="opls_140"} -64: type[18]={name="opls_287",nameB="opls_287"} -64: type[19]={name="opls_290",nameB="opls_290"} -64: type[20]={name="opls_290",nameB="opls_290"} -64: type[21]={name="opls_290",nameB="opls_290"} -64: type[22]={name="opls_235",nameB="opls_235"} -64: type[23]={name="opls_236",nameB="opls_236"} -64: type[24]={name="opls_238",nameB="opls_238"} -64: type[25]={name="opls_241",nameB="opls_241"} -64: type[26]={name="opls_224B",nameB="opls_224B"} -64: type[27]={name="opls_140",nameB="opls_140"} -64: type[28]={name="opls_137",nameB="opls_137"} -64: type[29]={name="opls_140",nameB="opls_140"} -64: type[30]={name="opls_135",nameB="opls_135"} -64: type[31]={name="opls_140",nameB="opls_140"} -64: type[32]={name="opls_140",nameB="opls_140"} -64: type[33]={name="opls_140",nameB="opls_140"} -64: type[34]={name="opls_135",nameB="opls_135"} -64: type[35]={name="opls_140",nameB="opls_140"} -64: type[36]={name="opls_140",nameB="opls_140"} -64: type[37]={name="opls_140",nameB="opls_140"} -64: type[38]={name="opls_235",nameB="opls_235"} -64: type[39]={name="opls_236",nameB="opls_236"} -64: type[40]={name="opls_238",nameB="opls_238"} -64: type[41]={name="opls_241",nameB="opls_241"} -64: type[42]={name="opls_224B",nameB="opls_224B"} -64: type[43]={name="opls_140",nameB="opls_140"} -64: type[44]={name="opls_149",nameB="opls_149"} -64: type[45]={name="opls_140",nameB="opls_140"} -64: type[46]={name="opls_140",nameB="opls_140"} -64: type[47]={name="opls_145",nameB="opls_145"} -64: type[48]={name="opls_145",nameB="opls_145"} -64: type[49]={name="opls_146",nameB="opls_146"} -64: type[50]={name="opls_145",nameB="opls_145"} -64: type[51]={name="opls_146",nameB="opls_146"} -64: type[52]={name="opls_145",nameB="opls_145"} -64: type[53]={name="opls_146",nameB="opls_146"} -64: type[54]={name="opls_145",nameB="opls_145"} -64: type[55]={name="opls_146",nameB="opls_146"} -64: type[56]={name="opls_145",nameB="opls_145"} -64: type[57]={name="opls_146",nameB="opls_146"} -64: type[58]={name="opls_235",nameB="opls_235"} -64: type[59]={name="opls_236",nameB="opls_236"} -64: type[60]={name="opls_238",nameB="opls_238"} -64: type[61]={name="opls_241",nameB="opls_241"} -64: type[62]={name="opls_223B",nameB="opls_223B"} -64: type[63]={name="opls_140",nameB="opls_140"} -64: type[64]={name="opls_140",nameB="opls_140"} -64: type[65]={name="opls_235",nameB="opls_235"} -64: type[66]={name="opls_236",nameB="opls_236"} -64: type[67]={name="opls_238",nameB="opls_238"} -64: type[68]={name="opls_241",nameB="opls_241"} -64: type[69]={name="opls_224B",nameB="opls_224B"} -64: type[70]={name="opls_140",nameB="opls_140"} -64: type[71]={name="opls_136",nameB="opls_136"} -64: type[72]={name="opls_140",nameB="opls_140"} -64: type[73]={name="opls_140",nameB="opls_140"} -64: type[74]={name="opls_308",nameB="opls_308"} -64: type[75]={name="opls_140",nameB="opls_140"} -64: type[76]={name="opls_140",nameB="opls_140"} -64: type[77]={name="opls_307",nameB="opls_307"} -64: type[78]={name="opls_140",nameB="opls_140"} -64: type[79]={name="opls_140",nameB="opls_140"} -64: type[80]={name="opls_303",nameB="opls_303"} -64: type[81]={name="opls_304",nameB="opls_304"} -64: type[82]={name="opls_302",nameB="opls_302"} -64: type[83]={name="opls_300",nameB="opls_300"} -64: type[84]={name="opls_301",nameB="opls_301"} -64: type[85]={name="opls_301",nameB="opls_301"} -64: type[86]={name="opls_300",nameB="opls_300"} -64: type[87]={name="opls_301",nameB="opls_301"} -64: type[88]={name="opls_301",nameB="opls_301"} -64: type[89]={name="opls_235",nameB="opls_235"} -64: type[90]={name="opls_236",nameB="opls_236"} -64: type[91]={name="opls_238",nameB="opls_238"} -64: type[92]={name="opls_241",nameB="opls_241"} -64: type[93]={name="opls_224B",nameB="opls_224B"} -64: type[94]={name="opls_140",nameB="opls_140"} -64: type[95]={name="opls_206",nameB="opls_206"} -64: type[96]={name="opls_140",nameB="opls_140"} -64: type[97]={name="opls_140",nameB="opls_140"} -64: type[98]={name="opls_200",nameB="opls_200"} -64: type[99]={name="opls_204",nameB="opls_204"} -64: type[100]={name="opls_235",nameB="opls_235"} -64: type[101]={name="opls_236",nameB="opls_236"} -64: type[102]={name="opls_238",nameB="opls_238"} -64: type[103]={name="opls_241",nameB="opls_241"} -64: type[104]={name="opls_224B",nameB="opls_224B"} -64: type[105]={name="opls_140",nameB="opls_140"} -64: type[106]={name="opls_136",nameB="opls_136"} -64: type[107]={name="opls_140",nameB="opls_140"} -64: type[108]={name="opls_140",nameB="opls_140"} -64: type[109]={name="opls_274",nameB="opls_274"} -64: type[110]={name="opls_140",nameB="opls_140"} -64: type[111]={name="opls_140",nameB="opls_140"} -64: type[112]={name="opls_271",nameB="opls_271"} -64: type[113]={name="opls_272",nameB="opls_272"} -64: type[114]={name="opls_272",nameB="opls_272"} -64: type[115]={name="opls_235",nameB="opls_235"} -64: type[116]={name="opls_236",nameB="opls_236"} -64: type[117]={name="opls_238",nameB="opls_238"} -64: type[118]={name="opls_241",nameB="opls_241"} -64: type[119]={name="opls_224B",nameB="opls_224B"} -64: type[120]={name="opls_140",nameB="opls_140"} -64: type[121]={name="opls_136",nameB="opls_136"} -64: type[122]={name="opls_140",nameB="opls_140"} -64: type[123]={name="opls_140",nameB="opls_140"} -64: type[124]={name="opls_137",nameB="opls_137"} -64: type[125]={name="opls_140",nameB="opls_140"} -64: type[126]={name="opls_135",nameB="opls_135"} -64: type[127]={name="opls_140",nameB="opls_140"} -64: type[128]={name="opls_140",nameB="opls_140"} -64: type[129]={name="opls_140",nameB="opls_140"} -64: type[130]={name="opls_135",nameB="opls_135"} -64: type[131]={name="opls_140",nameB="opls_140"} -64: type[132]={name="opls_140",nameB="opls_140"} -64: type[133]={name="opls_140",nameB="opls_140"} -64: type[134]={name="opls_235",nameB="opls_235"} -64: type[135]={name="opls_236",nameB="opls_236"} -64: type[136]={name="opls_238",nameB="opls_238"} -64: type[137]={name="opls_241",nameB="opls_241"} -64: type[138]={name="opls_224B",nameB="opls_224B"} -64: type[139]={name="opls_140",nameB="opls_140"} -64: type[140]={name="opls_135",nameB="opls_135"} -64: type[141]={name="opls_140",nameB="opls_140"} -64: type[142]={name="opls_140",nameB="opls_140"} -64: type[143]={name="opls_140",nameB="opls_140"} -64: type[144]={name="opls_235",nameB="opls_235"} -64: type[145]={name="opls_236",nameB="opls_236"} -64: type[146]={name="opls_238",nameB="opls_238"} -64: type[147]={name="opls_241",nameB="opls_241"} -64: type[148]={name="opls_224B",nameB="opls_224B"} -64: type[149]={name="opls_140",nameB="opls_140"} -64: type[150]={name="opls_135",nameB="opls_135"} -64: type[151]={name="opls_140",nameB="opls_140"} -64: type[152]={name="opls_140",nameB="opls_140"} -64: type[153]={name="opls_140",nameB="opls_140"} -64: type[154]={name="opls_235",nameB="opls_235"} -64: type[155]={name="opls_236",nameB="opls_236"} -64: residue (10): -64: residue[0]={name="LYS", nr=1, ic=' '} -64: residue[1]={name="VAL", nr=2, ic=' '} -64: residue[2]={name="PHE", nr=3, ic=' '} -64: residue[3]={name="GLY", nr=4, ic=' '} -64: residue[4]={name="ARG", nr=5, ic=' '} -64: residue[5]={name="CYS", nr=6, ic=' '} -64: residue[6]={name="GLU", nr=7, ic=' '} -64: residue[7]={name="LEU", nr=8, ic=' '} -64: residue[8]={name="ALA", nr=9, ic=' '} -64: residue[9]={name="ALA", nr=10, ic=' '} -64: excls: -64: numLists=156 -64: numElements=1828 -64: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -64: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -64: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -64: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} -64: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, -64: 23, 24, 25, 26} -64: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} -64: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, -64: 14, 15, 22, 23, 24} -64: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -64: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} -64: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -64: 16, 17, 18, 22} -64: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -64: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} -64: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, -64: 17, 18, 19, 20, 21} -64: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -64: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} -64: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, -64: 20, 21} -64: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -64: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -64: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} -64: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -64: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -64: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} -64: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, -64: 26, 27, 28, 38} -64: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} -64: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, -64: 30, 34, 38, 39, 40} -64: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} -64: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, -64: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} -64: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -64: 40} -64: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, -64: 34, 35, 36, 37, 38, 39, 40} -64: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -64: 36, 37, 38} -64: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -64: 36, 37, 38} -64: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -64: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -64: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} -64: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, -64: 36, 37, 38} -64: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -64: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -64: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} -64: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, -64: 40, 41, 42, 43, 44, 58} -64: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} -64: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, -64: 45, 46, 47, 58, 59, 60} -64: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} -64: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, -64: 48, 50, 58, 59, 60, 61, 62} -64: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -64: 60} -64: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, -64: 50, 51, 52, 54, 58, 59, 60} -64: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -64: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} -64: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, -64: 52, 53, 54, 55, 56, 58} -64: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, -64: 54, 56, 57} -64: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} -64: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, -64: 55, 56, 57} -64: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} -64: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} -64: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} -64: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} -64: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} -64: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} -64: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} -64: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, -64: 60, 61, 62, 63, 64, 65} -64: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} -64: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, -64: 65, 66, 67} -64: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} -64: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, -64: 68, 69} -64: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -64: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} -64: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, -64: 70, 71, 89} -64: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} -64: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, -64: 72, 73, 74, 89, 90, 91} -64: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} -64: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, -64: 75, 76, 77, 89, 90, 91, 92, 93} -64: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -64: 91} -64: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, -64: 77, 78, 79, 80, 89, 90, 91} -64: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -64: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} -64: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, -64: 79, 80, 81, 82, 89} -64: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -64: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} -64: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, -64: 81, 82, 83, 86} -64: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -64: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} -64: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, -64: 84, 85, 86, 87, 88} -64: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} -64: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, -64: 87, 88} -64: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -64: excls[84][num=6]={80, 82, 83, 84, 85, 86} -64: excls[85][num=6]={80, 82, 83, 84, 85, 86} -64: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} -64: excls[87][num=6]={80, 82, 83, 86, 87, 88} -64: excls[88][num=6]={80, 82, 83, 86, 87, 88} -64: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, -64: 91, 92, 93, 94, 95, 100} -64: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} -64: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, -64: 96, 97, 98, 100, 101, 102} -64: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} -64: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, -64: 99, 100, 101, 102, 103, 104} -64: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -64: 102} -64: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, -64: 101, 102} -64: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -64: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -64: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} -64: excls[99][num=6]={93, 95, 96, 97, 98, 99} -64: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, -64: 102, 103, 104, 105, 106, 115} -64: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} -64: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, -64: 106, 107, 108, 109, 115, 116, 117} -64: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} -64: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, -64: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} -64: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, -64: 115, 116, 117} -64: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -64: 110, 111, 112, 113, 114, 115, 116, 117} -64: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -64: 112, 115} -64: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, -64: 112, 115} -64: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, -64: 112, 113, 114, 115} -64: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -64: 114} -64: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -64: 114} -64: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, -64: 114} -64: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} -64: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} -64: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, -64: 115, 116, 117, 118, 119, 120, 121, 134} -64: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} -64: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, -64: 120, 121, 122, 123, 124, 134, 135, 136} -64: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} -64: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, -64: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} -64: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, -64: 134, 135, 136} -64: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, -64: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} -64: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -64: 130, 134} -64: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, -64: 130, 134} -64: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, -64: 127, 128, 129, 130, 131, 132, 133, 134} -64: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -64: 129, 130, 131, 132, 133} -64: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -64: 129, 130, 131, 132, 133} -64: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -64: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -64: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} -64: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, -64: 129, 130, 131, 132, 133} -64: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -64: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -64: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} -64: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, -64: 134, 135, 136, 137, 138, 139, 140, 144} -64: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} -64: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, -64: 139, 140, 141, 142, 143, 144, 145, 146} -64: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} -64: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, -64: 142, 143, 144, 145, 146, 147, 148} -64: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -64: 144, 145, 146} -64: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, -64: 144, 145, 146} -64: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -64: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -64: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} -64: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, -64: 144, 145, 146, 147, 148, 149, 150, 154} -64: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} -64: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, -64: 149, 150, 151, 152, 153, 154, 155} -64: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} -64: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, -64: 152, 153, 154, 155} -64: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -64: 154, 155} -64: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -64: 154, 155} -64: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -64: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -64: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} -64: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, -64: 154, 155} -64: excls[155][num=6]={146, 148, 149, 150, 154, 155} -64: Bond: -64: nr: 468 -64: iatoms: -64: 0 type=100 (BONDS) 0 1 -64: 1 type=100 (BONDS) 0 2 -64: 2 type=100 (BONDS) 0 3 -64: 3 type=101 (BONDS) 0 4 -64: 4 type=102 (BONDS) 4 5 -64: 5 type=103 (BONDS) 4 6 -64: 6 type=104 (BONDS) 4 22 -64: 7 type=102 (BONDS) 6 7 -64: 8 type=102 (BONDS) 6 8 -64: 9 type=103 (BONDS) 6 9 -64: 10 type=102 (BONDS) 9 10 -64: 11 type=102 (BONDS) 9 11 -64: 12 type=103 (BONDS) 9 12 -64: 13 type=102 (BONDS) 12 13 -64: 14 type=102 (BONDS) 12 14 -64: 15 type=103 (BONDS) 12 15 -64: 16 type=102 (BONDS) 15 16 -64: 17 type=102 (BONDS) 15 17 -64: 18 type=101 (BONDS) 15 18 -64: 19 type=100 (BONDS) 18 19 -64: 20 type=100 (BONDS) 18 20 -64: 21 type=100 (BONDS) 18 21 -64: 22 type=105 (BONDS) 22 23 -64: 23 type=106 (BONDS) 22 24 -64: 24 type=100 (BONDS) 24 25 -64: 25 type=107 (BONDS) 24 26 -64: 26 type=102 (BONDS) 26 27 -64: 27 type=103 (BONDS) 26 28 -64: 28 type=104 (BONDS) 26 38 -64: 29 type=102 (BONDS) 28 29 -64: 30 type=103 (BONDS) 28 30 -64: 31 type=103 (BONDS) 28 34 -64: 32 type=102 (BONDS) 30 31 -64: 33 type=102 (BONDS) 30 32 -64: 34 type=102 (BONDS) 30 33 -64: 35 type=102 (BONDS) 34 35 -64: 36 type=102 (BONDS) 34 36 -64: 37 type=102 (BONDS) 34 37 -64: 38 type=105 (BONDS) 38 39 -64: 39 type=106 (BONDS) 38 40 -64: 40 type=100 (BONDS) 40 41 -64: 41 type=107 (BONDS) 40 42 -64: 42 type=102 (BONDS) 42 43 -64: 43 type=103 (BONDS) 42 44 -64: 44 type=104 (BONDS) 42 58 -64: 45 type=102 (BONDS) 44 45 -64: 46 type=102 (BONDS) 44 46 -64: 47 type=108 (BONDS) 44 47 -64: 48 type=109 (BONDS) 47 48 -64: 49 type=109 (BONDS) 47 50 -64: 50 type=110 (BONDS) 48 49 -64: 51 type=109 (BONDS) 48 52 -64: 52 type=110 (BONDS) 50 51 -64: 53 type=109 (BONDS) 50 54 -64: 54 type=110 (BONDS) 52 53 -64: 55 type=109 (BONDS) 52 56 -64: 56 type=110 (BONDS) 54 55 -64: 57 type=109 (BONDS) 54 56 -64: 58 type=110 (BONDS) 56 57 -64: 59 type=105 (BONDS) 58 59 -64: 60 type=106 (BONDS) 58 60 -64: 61 type=100 (BONDS) 60 61 -64: 62 type=107 (BONDS) 60 62 -64: 63 type=102 (BONDS) 62 63 -64: 64 type=102 (BONDS) 62 64 -64: 65 type=104 (BONDS) 62 65 -64: 66 type=105 (BONDS) 65 66 -64: 67 type=106 (BONDS) 65 67 -64: 68 type=100 (BONDS) 67 68 -64: 69 type=107 (BONDS) 67 69 -64: 70 type=102 (BONDS) 69 70 -64: 71 type=103 (BONDS) 69 71 -64: 72 type=104 (BONDS) 69 89 -64: 73 type=102 (BONDS) 71 72 -64: 74 type=102 (BONDS) 71 73 -64: 75 type=103 (BONDS) 71 74 -64: 76 type=102 (BONDS) 74 75 -64: 77 type=102 (BONDS) 74 76 -64: 78 type=103 (BONDS) 74 77 -64: 79 type=102 (BONDS) 77 78 -64: 80 type=102 (BONDS) 77 79 -64: 81 type=111 (BONDS) 77 80 -64: 82 type=100 (BONDS) 80 81 -64: 83 type=112 (BONDS) 80 82 -64: 84 type=112 (BONDS) 82 83 -64: 85 type=112 (BONDS) 82 86 -64: 86 type=100 (BONDS) 83 84 -64: 87 type=100 (BONDS) 83 85 -64: 88 type=100 (BONDS) 86 87 -64: 89 type=100 (BONDS) 86 88 -64: 90 type=105 (BONDS) 89 90 -64: 91 type=106 (BONDS) 89 91 -64: 92 type=100 (BONDS) 91 92 -64: 93 type=107 (BONDS) 91 93 -64: 94 type=102 (BONDS) 93 94 -64: 95 type=103 (BONDS) 93 95 -64: 96 type=104 (BONDS) 93 100 -64: 97 type=102 (BONDS) 95 96 -64: 98 type=102 (BONDS) 95 97 -64: 99 type=113 (BONDS) 95 98 -64: 100 type=114 (BONDS) 98 99 -64: 101 type=105 (BONDS) 100 101 -64: 102 type=106 (BONDS) 100 102 -64: 103 type=100 (BONDS) 102 103 -64: 104 type=107 (BONDS) 102 104 -64: 105 type=102 (BONDS) 104 105 -64: 106 type=103 (BONDS) 104 106 -64: 107 type=104 (BONDS) 104 115 -64: 108 type=102 (BONDS) 106 107 -64: 109 type=102 (BONDS) 106 108 -64: 110 type=103 (BONDS) 106 109 -64: 111 type=102 (BONDS) 109 110 -64: 112 type=102 (BONDS) 109 111 -64: 113 type=104 (BONDS) 109 112 -64: 114 type=115 (BONDS) 112 113 -64: 115 type=115 (BONDS) 112 114 -64: 116 type=105 (BONDS) 115 116 -64: 117 type=106 (BONDS) 115 117 -64: 118 type=100 (BONDS) 117 118 -64: 119 type=107 (BONDS) 117 119 -64: 120 type=102 (BONDS) 119 120 -64: 121 type=103 (BONDS) 119 121 -64: 122 type=104 (BONDS) 119 134 -64: 123 type=102 (BONDS) 121 122 -64: 124 type=102 (BONDS) 121 123 -64: 125 type=103 (BONDS) 121 124 -64: 126 type=102 (BONDS) 124 125 -64: 127 type=103 (BONDS) 124 126 -64: 128 type=103 (BONDS) 124 130 -64: 129 type=102 (BONDS) 126 127 -64: 130 type=102 (BONDS) 126 128 -64: 131 type=102 (BONDS) 126 129 -64: 132 type=102 (BONDS) 130 131 -64: 133 type=102 (BONDS) 130 132 -64: 134 type=102 (BONDS) 130 133 -64: 135 type=105 (BONDS) 134 135 -64: 136 type=106 (BONDS) 134 136 -64: 137 type=100 (BONDS) 136 137 -64: 138 type=107 (BONDS) 136 138 -64: 139 type=102 (BONDS) 138 139 -64: 140 type=103 (BONDS) 138 140 -64: 141 type=104 (BONDS) 138 144 -64: 142 type=102 (BONDS) 140 141 -64: 143 type=102 (BONDS) 140 142 -64: 144 type=102 (BONDS) 140 143 -64: 145 type=105 (BONDS) 144 145 -64: 146 type=106 (BONDS) 144 146 -64: 147 type=100 (BONDS) 146 147 -64: 148 type=107 (BONDS) 146 148 -64: 149 type=102 (BONDS) 148 149 -64: 150 type=103 (BONDS) 148 150 -64: 151 type=104 (BONDS) 148 154 -64: 152 type=102 (BONDS) 150 151 -64: 153 type=102 (BONDS) 150 152 -64: 154 type=102 (BONDS) 150 153 -64: 155 type=105 (BONDS) 154 155 -64: G96Bond: -64: nr: 0 -64: Morse: -64: nr: 0 -64: Cubic Bonds: -64: nr: 0 -64: Connect Bonds: -64: nr: 0 -64: Harmonic Pot.: -64: nr: 0 -64: FENE Bonds: -64: nr: 0 -64: Tab. Bonds: -64: nr: 0 -64: Tab. Bonds NC: -64: nr: 0 -64: Restraint Pot.: -64: nr: 0 -64: Angle: -64: nr: 1124 -64: iatoms: -64: 0 type=116 (ANGLES) 1 0 2 -64: 1 type=116 (ANGLES) 1 0 3 -64: 2 type=116 (ANGLES) 1 0 4 -64: 3 type=116 (ANGLES) 2 0 3 -64: 4 type=116 (ANGLES) 2 0 4 -64: 5 type=116 (ANGLES) 3 0 4 -64: 6 type=116 (ANGLES) 0 4 5 -64: 7 type=117 (ANGLES) 0 4 6 -64: 8 type=117 (ANGLES) 0 4 22 -64: 9 type=118 (ANGLES) 5 4 6 -64: 10 type=116 (ANGLES) 5 4 22 -64: 11 type=119 (ANGLES) 6 4 22 -64: 12 type=118 (ANGLES) 4 6 7 -64: 13 type=118 (ANGLES) 4 6 8 -64: 14 type=120 (ANGLES) 4 6 9 -64: 15 type=121 (ANGLES) 7 6 8 -64: 16 type=118 (ANGLES) 7 6 9 -64: 17 type=118 (ANGLES) 8 6 9 -64: 18 type=118 (ANGLES) 6 9 10 -64: 19 type=118 (ANGLES) 6 9 11 -64: 20 type=120 (ANGLES) 6 9 12 -64: 21 type=121 (ANGLES) 10 9 11 -64: 22 type=118 (ANGLES) 10 9 12 -64: 23 type=118 (ANGLES) 11 9 12 -64: 24 type=118 (ANGLES) 9 12 13 -64: 25 type=118 (ANGLES) 9 12 14 -64: 26 type=120 (ANGLES) 9 12 15 -64: 27 type=121 (ANGLES) 13 12 14 -64: 28 type=118 (ANGLES) 13 12 15 -64: 29 type=118 (ANGLES) 14 12 15 -64: 30 type=118 (ANGLES) 12 15 16 -64: 31 type=118 (ANGLES) 12 15 17 -64: 32 type=117 (ANGLES) 12 15 18 -64: 33 type=121 (ANGLES) 16 15 17 -64: 34 type=116 (ANGLES) 16 15 18 -64: 35 type=116 (ANGLES) 17 15 18 -64: 36 type=116 (ANGLES) 15 18 19 -64: 37 type=116 (ANGLES) 15 18 20 -64: 38 type=116 (ANGLES) 15 18 21 -64: 39 type=116 (ANGLES) 19 18 20 -64: 40 type=116 (ANGLES) 19 18 21 -64: 41 type=116 (ANGLES) 20 18 21 -64: 42 type=122 (ANGLES) 4 22 23 -64: 43 type=123 (ANGLES) 4 22 24 -64: 44 type=124 (ANGLES) 23 22 24 -64: 45 type=125 (ANGLES) 22 24 25 -64: 46 type=126 (ANGLES) 22 24 26 -64: 47 type=127 (ANGLES) 25 24 26 -64: 48 type=116 (ANGLES) 24 26 27 -64: 49 type=128 (ANGLES) 24 26 28 -64: 50 type=129 (ANGLES) 24 26 38 -64: 51 type=118 (ANGLES) 27 26 28 -64: 52 type=116 (ANGLES) 27 26 38 -64: 53 type=119 (ANGLES) 28 26 38 -64: 54 type=118 (ANGLES) 26 28 29 -64: 55 type=120 (ANGLES) 26 28 30 -64: 56 type=120 (ANGLES) 26 28 34 -64: 57 type=118 (ANGLES) 29 28 30 -64: 58 type=118 (ANGLES) 29 28 34 -64: 59 type=120 (ANGLES) 30 28 34 -64: 60 type=118 (ANGLES) 28 30 31 -64: 61 type=118 (ANGLES) 28 30 32 -64: 62 type=118 (ANGLES) 28 30 33 -64: 63 type=121 (ANGLES) 31 30 32 -64: 64 type=121 (ANGLES) 31 30 33 -64: 65 type=121 (ANGLES) 32 30 33 -64: 66 type=118 (ANGLES) 28 34 35 -64: 67 type=118 (ANGLES) 28 34 36 -64: 68 type=118 (ANGLES) 28 34 37 -64: 69 type=121 (ANGLES) 35 34 36 -64: 70 type=121 (ANGLES) 35 34 37 -64: 71 type=121 (ANGLES) 36 34 37 -64: 72 type=122 (ANGLES) 26 38 39 -64: 73 type=123 (ANGLES) 26 38 40 -64: 74 type=124 (ANGLES) 39 38 40 -64: 75 type=125 (ANGLES) 38 40 41 -64: 76 type=126 (ANGLES) 38 40 42 -64: 77 type=127 (ANGLES) 41 40 42 -64: 78 type=116 (ANGLES) 40 42 43 -64: 79 type=128 (ANGLES) 40 42 44 -64: 80 type=129 (ANGLES) 40 42 58 -64: 81 type=118 (ANGLES) 43 42 44 -64: 82 type=116 (ANGLES) 43 42 58 -64: 83 type=119 (ANGLES) 44 42 58 -64: 84 type=118 (ANGLES) 42 44 45 -64: 85 type=118 (ANGLES) 42 44 46 -64: 86 type=130 (ANGLES) 42 44 47 -64: 87 type=121 (ANGLES) 45 44 46 -64: 88 type=116 (ANGLES) 45 44 47 -64: 89 type=116 (ANGLES) 46 44 47 -64: 90 type=131 (ANGLES) 44 47 48 -64: 91 type=131 (ANGLES) 44 47 50 -64: 92 type=132 (ANGLES) 48 47 50 -64: 93 type=133 (ANGLES) 47 48 49 -64: 94 type=132 (ANGLES) 47 48 52 -64: 95 type=133 (ANGLES) 49 48 52 -64: 96 type=133 (ANGLES) 47 50 51 -64: 97 type=132 (ANGLES) 47 50 54 -64: 98 type=133 (ANGLES) 51 50 54 -64: 99 type=133 (ANGLES) 48 52 53 -64: 100 type=132 (ANGLES) 48 52 56 -64: 101 type=133 (ANGLES) 53 52 56 -64: 102 type=133 (ANGLES) 50 54 55 -64: 103 type=132 (ANGLES) 50 54 56 -64: 104 type=133 (ANGLES) 55 54 56 -64: 105 type=132 (ANGLES) 52 56 54 -64: 106 type=133 (ANGLES) 52 56 57 -64: 107 type=133 (ANGLES) 54 56 57 -64: 108 type=122 (ANGLES) 42 58 59 -64: 109 type=123 (ANGLES) 42 58 60 -64: 110 type=124 (ANGLES) 59 58 60 -64: 111 type=125 (ANGLES) 58 60 61 -64: 112 type=126 (ANGLES) 58 60 62 -64: 113 type=127 (ANGLES) 61 60 62 -64: 114 type=116 (ANGLES) 60 62 63 -64: 115 type=116 (ANGLES) 60 62 64 -64: 116 type=129 (ANGLES) 60 62 65 -64: 117 type=121 (ANGLES) 63 62 64 -64: 118 type=116 (ANGLES) 63 62 65 -64: 119 type=116 (ANGLES) 64 62 65 -64: 120 type=122 (ANGLES) 62 65 66 -64: 121 type=123 (ANGLES) 62 65 67 -64: 122 type=124 (ANGLES) 66 65 67 -64: 123 type=125 (ANGLES) 65 67 68 -64: 124 type=126 (ANGLES) 65 67 69 -64: 125 type=127 (ANGLES) 68 67 69 -64: 126 type=116 (ANGLES) 67 69 70 -64: 127 type=128 (ANGLES) 67 69 71 -64: 128 type=129 (ANGLES) 67 69 89 -64: 129 type=118 (ANGLES) 70 69 71 -64: 130 type=116 (ANGLES) 70 69 89 -64: 131 type=119 (ANGLES) 71 69 89 -64: 132 type=118 (ANGLES) 69 71 72 -64: 133 type=118 (ANGLES) 69 71 73 -64: 134 type=120 (ANGLES) 69 71 74 -64: 135 type=121 (ANGLES) 72 71 73 -64: 136 type=118 (ANGLES) 72 71 74 -64: 137 type=118 (ANGLES) 73 71 74 -64: 138 type=118 (ANGLES) 71 74 75 -64: 139 type=118 (ANGLES) 71 74 76 -64: 140 type=120 (ANGLES) 71 74 77 -64: 141 type=121 (ANGLES) 75 74 76 -64: 142 type=118 (ANGLES) 75 74 77 -64: 143 type=118 (ANGLES) 76 74 77 -64: 144 type=118 (ANGLES) 74 77 78 -64: 145 type=118 (ANGLES) 74 77 79 -64: 146 type=117 (ANGLES) 74 77 80 -64: 147 type=121 (ANGLES) 78 77 79 -64: 148 type=116 (ANGLES) 78 77 80 -64: 149 type=116 (ANGLES) 79 77 80 -64: 150 type=134 (ANGLES) 77 80 81 -64: 151 type=135 (ANGLES) 77 80 82 -64: 152 type=133 (ANGLES) 81 80 82 -64: 153 type=131 (ANGLES) 80 82 83 -64: 154 type=131 (ANGLES) 80 82 86 -64: 155 type=131 (ANGLES) 83 82 86 -64: 156 type=133 (ANGLES) 82 83 84 -64: 157 type=133 (ANGLES) 82 83 85 -64: 158 type=133 (ANGLES) 84 83 85 -64: 159 type=133 (ANGLES) 82 86 87 -64: 160 type=133 (ANGLES) 82 86 88 -64: 161 type=133 (ANGLES) 87 86 88 -64: 162 type=122 (ANGLES) 69 89 90 -64: 163 type=123 (ANGLES) 69 89 91 -64: 164 type=124 (ANGLES) 90 89 91 -64: 165 type=125 (ANGLES) 89 91 92 -64: 166 type=126 (ANGLES) 89 91 93 -64: 167 type=127 (ANGLES) 92 91 93 -64: 168 type=116 (ANGLES) 91 93 94 -64: 169 type=128 (ANGLES) 91 93 95 -64: 170 type=129 (ANGLES) 91 93 100 -64: 171 type=118 (ANGLES) 94 93 95 -64: 172 type=116 (ANGLES) 94 93 100 -64: 173 type=119 (ANGLES) 95 93 100 -64: 174 type=118 (ANGLES) 93 95 96 -64: 175 type=118 (ANGLES) 93 95 97 -64: 176 type=136 (ANGLES) 93 95 98 -64: 177 type=121 (ANGLES) 96 95 97 -64: 178 type=116 (ANGLES) 96 95 98 -64: 179 type=116 (ANGLES) 97 95 98 -64: 180 type=137 (ANGLES) 95 98 99 -64: 181 type=122 (ANGLES) 93 100 101 -64: 182 type=123 (ANGLES) 93 100 102 -64: 183 type=124 (ANGLES) 101 100 102 -64: 184 type=125 (ANGLES) 100 102 103 -64: 185 type=126 (ANGLES) 100 102 104 -64: 186 type=127 (ANGLES) 103 102 104 -64: 187 type=116 (ANGLES) 102 104 105 -64: 188 type=128 (ANGLES) 102 104 106 -64: 189 type=129 (ANGLES) 102 104 115 -64: 190 type=118 (ANGLES) 105 104 106 -64: 191 type=116 (ANGLES) 105 104 115 -64: 192 type=119 (ANGLES) 106 104 115 -64: 193 type=118 (ANGLES) 104 106 107 -64: 194 type=118 (ANGLES) 104 106 108 -64: 195 type=120 (ANGLES) 104 106 109 -64: 196 type=121 (ANGLES) 107 106 108 -64: 197 type=118 (ANGLES) 107 106 109 -64: 198 type=118 (ANGLES) 108 106 109 -64: 199 type=118 (ANGLES) 106 109 110 -64: 200 type=118 (ANGLES) 106 109 111 -64: 201 type=119 (ANGLES) 106 109 112 -64: 202 type=121 (ANGLES) 110 109 111 -64: 203 type=116 (ANGLES) 110 109 112 -64: 204 type=116 (ANGLES) 111 109 112 -64: 205 type=138 (ANGLES) 109 112 113 -64: 206 type=138 (ANGLES) 109 112 114 -64: 207 type=139 (ANGLES) 113 112 114 -64: 208 type=122 (ANGLES) 104 115 116 -64: 209 type=123 (ANGLES) 104 115 117 -64: 210 type=124 (ANGLES) 116 115 117 -64: 211 type=125 (ANGLES) 115 117 118 -64: 212 type=126 (ANGLES) 115 117 119 -64: 213 type=127 (ANGLES) 118 117 119 -64: 214 type=116 (ANGLES) 117 119 120 -64: 215 type=128 (ANGLES) 117 119 121 -64: 216 type=129 (ANGLES) 117 119 134 -64: 217 type=118 (ANGLES) 120 119 121 -64: 218 type=116 (ANGLES) 120 119 134 -64: 219 type=119 (ANGLES) 121 119 134 -64: 220 type=118 (ANGLES) 119 121 122 -64: 221 type=118 (ANGLES) 119 121 123 -64: 222 type=120 (ANGLES) 119 121 124 -64: 223 type=121 (ANGLES) 122 121 123 -64: 224 type=118 (ANGLES) 122 121 124 -64: 225 type=118 (ANGLES) 123 121 124 -64: 226 type=118 (ANGLES) 121 124 125 -64: 227 type=120 (ANGLES) 121 124 126 -64: 228 type=120 (ANGLES) 121 124 130 -64: 229 type=118 (ANGLES) 125 124 126 -64: 230 type=118 (ANGLES) 125 124 130 -64: 231 type=120 (ANGLES) 126 124 130 -64: 232 type=118 (ANGLES) 124 126 127 -64: 233 type=118 (ANGLES) 124 126 128 -64: 234 type=118 (ANGLES) 124 126 129 -64: 235 type=121 (ANGLES) 127 126 128 -64: 236 type=121 (ANGLES) 127 126 129 -64: 237 type=121 (ANGLES) 128 126 129 -64: 238 type=118 (ANGLES) 124 130 131 -64: 239 type=118 (ANGLES) 124 130 132 -64: 240 type=118 (ANGLES) 124 130 133 -64: 241 type=121 (ANGLES) 131 130 132 -64: 242 type=121 (ANGLES) 131 130 133 -64: 243 type=121 (ANGLES) 132 130 133 -64: 244 type=122 (ANGLES) 119 134 135 -64: 245 type=123 (ANGLES) 119 134 136 -64: 246 type=124 (ANGLES) 135 134 136 -64: 247 type=125 (ANGLES) 134 136 137 -64: 248 type=126 (ANGLES) 134 136 138 -64: 249 type=127 (ANGLES) 137 136 138 -64: 250 type=116 (ANGLES) 136 138 139 -64: 251 type=128 (ANGLES) 136 138 140 -64: 252 type=129 (ANGLES) 136 138 144 -64: 253 type=118 (ANGLES) 139 138 140 -64: 254 type=116 (ANGLES) 139 138 144 -64: 255 type=119 (ANGLES) 140 138 144 -64: 256 type=118 (ANGLES) 138 140 141 -64: 257 type=118 (ANGLES) 138 140 142 -64: 258 type=118 (ANGLES) 138 140 143 -64: 259 type=121 (ANGLES) 141 140 142 -64: 260 type=121 (ANGLES) 141 140 143 -64: 261 type=121 (ANGLES) 142 140 143 -64: 262 type=122 (ANGLES) 138 144 145 -64: 263 type=123 (ANGLES) 138 144 146 -64: 264 type=124 (ANGLES) 145 144 146 -64: 265 type=125 (ANGLES) 144 146 147 -64: 266 type=126 (ANGLES) 144 146 148 -64: 267 type=127 (ANGLES) 147 146 148 -64: 268 type=116 (ANGLES) 146 148 149 -64: 269 type=128 (ANGLES) 146 148 150 -64: 270 type=129 (ANGLES) 146 148 154 -64: 271 type=118 (ANGLES) 149 148 150 -64: 272 type=116 (ANGLES) 149 148 154 -64: 273 type=119 (ANGLES) 150 148 154 -64: 274 type=118 (ANGLES) 148 150 151 -64: 275 type=118 (ANGLES) 148 150 152 -64: 276 type=118 (ANGLES) 148 150 153 -64: 277 type=121 (ANGLES) 151 150 152 -64: 278 type=121 (ANGLES) 151 150 153 -64: 279 type=121 (ANGLES) 152 150 153 -64: 280 type=122 (ANGLES) 148 154 155 -64: G96Angle: -64: nr: 0 -64: Restr. Angles: -64: nr: 0 -64: Lin. Angle: -64: nr: 0 -64: Bond-Cross: -64: nr: 0 -64: BA-Cross: -64: nr: 0 -64: U-B: -64: nr: 0 -64: Quartic Angles: -64: nr: 0 -64: Tab. Angles: -64: nr: 0 -64: Proper Dih.: -64: nr: 145 -64: iatoms: -64: 0 type=140 (PDIHS) 4 24 22 23 -64: 1 type=141 (PDIHS) 22 26 24 25 -64: 2 type=140 (PDIHS) 26 40 38 39 -64: 3 type=141 (PDIHS) 38 42 40 41 -64: 4 type=140 (PDIHS) 42 60 58 59 -64: 5 type=142 (PDIHS) 44 47 50 48 -64: 6 type=142 (PDIHS) 47 52 48 49 -64: 7 type=142 (PDIHS) 47 54 50 51 -64: 8 type=142 (PDIHS) 48 56 52 53 -64: 9 type=142 (PDIHS) 50 56 54 55 -64: 10 type=142 (PDIHS) 52 54 56 57 -64: 11 type=141 (PDIHS) 58 62 60 61 -64: 12 type=140 (PDIHS) 62 67 65 66 -64: 13 type=141 (PDIHS) 65 69 67 68 -64: 14 type=140 (PDIHS) 69 91 89 90 -64: 15 type=141 (PDIHS) 77 82 80 81 -64: 16 type=140 (PDIHS) 80 83 82 86 -64: 17 type=141 (PDIHS) 82 84 83 85 -64: 18 type=141 (PDIHS) 82 87 86 88 -64: 19 type=141 (PDIHS) 89 93 91 92 -64: 20 type=140 (PDIHS) 93 102 100 101 -64: 21 type=141 (PDIHS) 100 104 102 103 -64: 22 type=140 (PDIHS) 104 117 115 116 -64: 23 type=140 (PDIHS) 109 113 112 114 -64: 24 type=141 (PDIHS) 115 119 117 118 -64: 25 type=140 (PDIHS) 119 136 134 135 -64: 26 type=141 (PDIHS) 134 138 136 137 -64: 27 type=140 (PDIHS) 138 146 144 145 -64: 28 type=141 (PDIHS) 144 148 146 147 -64: Ryckaert-Bell.: -64: nr: 1565 -64: iatoms: -64: 0 type=143 (RBDIHS) 1 0 4 5 -64: 1 type=144 (RBDIHS) 1 0 4 6 -64: 2 type=144 (RBDIHS) 1 0 4 22 -64: 3 type=143 (RBDIHS) 2 0 4 5 -64: 4 type=144 (RBDIHS) 2 0 4 6 -64: 5 type=144 (RBDIHS) 2 0 4 22 -64: 6 type=143 (RBDIHS) 3 0 4 5 -64: 7 type=144 (RBDIHS) 3 0 4 6 -64: 8 type=144 (RBDIHS) 3 0 4 22 -64: 9 type=145 (RBDIHS) 0 4 6 9 -64: 10 type=146 (RBDIHS) 22 4 6 9 -64: 11 type=147 (RBDIHS) 0 4 6 7 -64: 12 type=147 (RBDIHS) 0 4 6 8 -64: 13 type=148 (RBDIHS) 5 4 6 7 -64: 14 type=148 (RBDIHS) 5 4 6 8 -64: 15 type=148 (RBDIHS) 5 4 6 9 -64: 16 type=149 (RBDIHS) 22 4 6 7 -64: 17 type=149 (RBDIHS) 22 4 6 8 -64: 18 type=150 (RBDIHS) 0 4 22 24 -64: 19 type=151 (RBDIHS) 6 4 22 24 -64: 20 type=148 (RBDIHS) 4 6 9 10 -64: 21 type=148 (RBDIHS) 4 6 9 11 -64: 22 type=152 (RBDIHS) 4 6 9 12 -64: 23 type=148 (RBDIHS) 7 6 9 10 -64: 24 type=148 (RBDIHS) 7 6 9 11 -64: 25 type=148 (RBDIHS) 7 6 9 12 -64: 26 type=148 (RBDIHS) 8 6 9 10 -64: 27 type=148 (RBDIHS) 8 6 9 11 -64: 28 type=148 (RBDIHS) 8 6 9 12 -64: 29 type=148 (RBDIHS) 6 9 12 13 -64: 30 type=148 (RBDIHS) 6 9 12 14 -64: 31 type=152 (RBDIHS) 6 9 12 15 -64: 32 type=148 (RBDIHS) 10 9 12 13 -64: 33 type=148 (RBDIHS) 10 9 12 14 -64: 34 type=148 (RBDIHS) 10 9 12 15 -64: 35 type=148 (RBDIHS) 11 9 12 13 -64: 36 type=148 (RBDIHS) 11 9 12 14 -64: 37 type=148 (RBDIHS) 11 9 12 15 -64: 38 type=148 (RBDIHS) 9 12 15 16 -64: 39 type=148 (RBDIHS) 9 12 15 17 -64: 40 type=153 (RBDIHS) 9 12 15 18 -64: 41 type=148 (RBDIHS) 13 12 15 16 -64: 42 type=148 (RBDIHS) 13 12 15 17 -64: 43 type=154 (RBDIHS) 13 12 15 18 -64: 44 type=148 (RBDIHS) 14 12 15 16 -64: 45 type=148 (RBDIHS) 14 12 15 17 -64: 46 type=154 (RBDIHS) 14 12 15 18 -64: 47 type=144 (RBDIHS) 12 15 18 19 -64: 48 type=144 (RBDIHS) 12 15 18 20 -64: 49 type=144 (RBDIHS) 12 15 18 21 -64: 50 type=143 (RBDIHS) 16 15 18 19 -64: 51 type=143 (RBDIHS) 16 15 18 20 -64: 52 type=143 (RBDIHS) 16 15 18 21 -64: 53 type=143 (RBDIHS) 17 15 18 19 -64: 54 type=143 (RBDIHS) 17 15 18 20 -64: 55 type=143 (RBDIHS) 17 15 18 21 -64: 56 type=155 (RBDIHS) 4 22 24 25 -64: 57 type=156 (RBDIHS) 4 22 24 26 -64: 58 type=155 (RBDIHS) 23 22 24 25 -64: 59 type=157 (RBDIHS) 23 22 24 26 -64: 60 type=158 (RBDIHS) 22 24 26 28 -64: 61 type=159 (RBDIHS) 22 24 26 38 -64: 62 type=160 (RBDIHS) 24 26 28 30 -64: 63 type=160 (RBDIHS) 24 26 28 34 -64: 64 type=161 (RBDIHS) 38 26 28 30 -64: 65 type=161 (RBDIHS) 38 26 28 34 -64: 66 type=147 (RBDIHS) 24 26 28 29 -64: 67 type=148 (RBDIHS) 27 26 28 29 -64: 68 type=148 (RBDIHS) 27 26 28 30 -64: 69 type=148 (RBDIHS) 27 26 28 34 -64: 70 type=149 (RBDIHS) 38 26 28 29 -64: 71 type=150 (RBDIHS) 24 26 38 40 -64: 72 type=151 (RBDIHS) 28 26 38 40 -64: 73 type=148 (RBDIHS) 26 28 30 31 -64: 74 type=148 (RBDIHS) 26 28 30 32 -64: 75 type=148 (RBDIHS) 26 28 30 33 -64: 76 type=148 (RBDIHS) 29 28 30 31 -64: 77 type=148 (RBDIHS) 29 28 30 32 -64: 78 type=148 (RBDIHS) 29 28 30 33 -64: 79 type=148 (RBDIHS) 34 28 30 31 -64: 80 type=148 (RBDIHS) 34 28 30 32 -64: 81 type=148 (RBDIHS) 34 28 30 33 -64: 82 type=148 (RBDIHS) 26 28 34 35 -64: 83 type=148 (RBDIHS) 26 28 34 36 -64: 84 type=148 (RBDIHS) 26 28 34 37 -64: 85 type=148 (RBDIHS) 29 28 34 35 -64: 86 type=148 (RBDIHS) 29 28 34 36 -64: 87 type=148 (RBDIHS) 29 28 34 37 -64: 88 type=148 (RBDIHS) 30 28 34 35 -64: 89 type=148 (RBDIHS) 30 28 34 36 -64: 90 type=148 (RBDIHS) 30 28 34 37 -64: 91 type=155 (RBDIHS) 26 38 40 41 -64: 92 type=156 (RBDIHS) 26 38 40 42 -64: 93 type=155 (RBDIHS) 39 38 40 41 -64: 94 type=157 (RBDIHS) 39 38 40 42 -64: 95 type=158 (RBDIHS) 38 40 42 44 -64: 96 type=159 (RBDIHS) 38 40 42 58 -64: 97 type=147 (RBDIHS) 40 42 44 45 -64: 98 type=147 (RBDIHS) 40 42 44 46 -64: 99 type=162 (RBDIHS) 40 42 44 47 -64: 100 type=148 (RBDIHS) 43 42 44 45 -64: 101 type=148 (RBDIHS) 43 42 44 46 -64: 102 type=163 (RBDIHS) 43 42 44 47 -64: 103 type=149 (RBDIHS) 58 42 44 45 -64: 104 type=149 (RBDIHS) 58 42 44 46 -64: 105 type=164 (RBDIHS) 58 42 44 47 -64: 106 type=150 (RBDIHS) 40 42 58 60 -64: 107 type=151 (RBDIHS) 44 42 58 60 -64: 108 type=165 (RBDIHS) 44 47 48 49 -64: 109 type=165 (RBDIHS) 44 47 48 52 -64: 110 type=165 (RBDIHS) 50 47 48 49 -64: 111 type=165 (RBDIHS) 50 47 48 52 -64: 112 type=165 (RBDIHS) 44 47 50 51 -64: 113 type=165 (RBDIHS) 44 47 50 54 -64: 114 type=165 (RBDIHS) 48 47 50 51 -64: 115 type=165 (RBDIHS) 48 47 50 54 -64: 116 type=165 (RBDIHS) 47 48 52 53 -64: 117 type=165 (RBDIHS) 47 48 52 56 -64: 118 type=165 (RBDIHS) 49 48 52 53 -64: 119 type=165 (RBDIHS) 49 48 52 56 -64: 120 type=165 (RBDIHS) 47 50 54 55 -64: 121 type=165 (RBDIHS) 47 50 54 56 -64: 122 type=165 (RBDIHS) 51 50 54 55 -64: 123 type=165 (RBDIHS) 51 50 54 56 -64: 124 type=165 (RBDIHS) 48 52 56 54 -64: 125 type=165 (RBDIHS) 48 52 56 57 -64: 126 type=165 (RBDIHS) 53 52 56 54 -64: 127 type=165 (RBDIHS) 53 52 56 57 -64: 128 type=165 (RBDIHS) 50 54 56 52 -64: 129 type=165 (RBDIHS) 50 54 56 57 -64: 130 type=165 (RBDIHS) 55 54 56 52 -64: 131 type=165 (RBDIHS) 55 54 56 57 -64: 132 type=155 (RBDIHS) 42 58 60 61 -64: 133 type=156 (RBDIHS) 42 58 60 62 -64: 134 type=155 (RBDIHS) 59 58 60 61 -64: 135 type=157 (RBDIHS) 59 58 60 62 -64: 136 type=159 (RBDIHS) 58 60 62 65 -64: 137 type=150 (RBDIHS) 60 62 65 67 -64: 138 type=155 (RBDIHS) 62 65 67 68 -64: 139 type=156 (RBDIHS) 62 65 67 69 -64: 140 type=155 (RBDIHS) 66 65 67 68 -64: 141 type=157 (RBDIHS) 66 65 67 69 -64: 142 type=158 (RBDIHS) 65 67 69 71 -64: 143 type=159 (RBDIHS) 65 67 69 89 -64: 144 type=166 (RBDIHS) 67 69 71 74 -64: 145 type=167 (RBDIHS) 89 69 71 74 -64: 146 type=147 (RBDIHS) 67 69 71 72 -64: 147 type=147 (RBDIHS) 67 69 71 73 -64: 148 type=148 (RBDIHS) 70 69 71 72 -64: 149 type=148 (RBDIHS) 70 69 71 73 -64: 150 type=148 (RBDIHS) 70 69 71 74 -64: 151 type=149 (RBDIHS) 89 69 71 72 -64: 152 type=149 (RBDIHS) 89 69 71 73 -64: 153 type=150 (RBDIHS) 67 69 89 91 -64: 154 type=151 (RBDIHS) 71 69 89 91 -64: 155 type=148 (RBDIHS) 69 71 74 75 -64: 156 type=148 (RBDIHS) 69 71 74 76 -64: 157 type=152 (RBDIHS) 69 71 74 77 -64: 158 type=148 (RBDIHS) 72 71 74 75 -64: 159 type=148 (RBDIHS) 72 71 74 76 -64: 160 type=148 (RBDIHS) 72 71 74 77 -64: 161 type=148 (RBDIHS) 73 71 74 75 -64: 162 type=148 (RBDIHS) 73 71 74 76 -64: 163 type=148 (RBDIHS) 73 71 74 77 -64: 164 type=148 (RBDIHS) 71 74 77 78 -64: 165 type=148 (RBDIHS) 71 74 77 79 -64: 166 type=153 (RBDIHS) 71 74 77 80 -64: 167 type=148 (RBDIHS) 75 74 77 78 -64: 168 type=148 (RBDIHS) 75 74 77 79 -64: 169 type=168 (RBDIHS) 75 74 77 80 -64: 170 type=148 (RBDIHS) 76 74 77 78 -64: 171 type=148 (RBDIHS) 76 74 77 79 -64: 172 type=168 (RBDIHS) 76 74 77 80 -64: 173 type=169 (RBDIHS) 74 77 80 81 -64: 174 type=170 (RBDIHS) 74 77 80 82 -64: 175 type=171 (RBDIHS) 78 77 80 82 -64: 176 type=171 (RBDIHS) 79 77 80 82 -64: 177 type=172 (RBDIHS) 77 80 82 83 -64: 178 type=172 (RBDIHS) 77 80 82 86 -64: 179 type=173 (RBDIHS) 81 80 82 83 -64: 180 type=173 (RBDIHS) 81 80 82 86 -64: 181 type=173 (RBDIHS) 80 82 83 84 -64: 182 type=173 (RBDIHS) 80 82 83 85 -64: 183 type=173 (RBDIHS) 86 82 83 84 -64: 184 type=173 (RBDIHS) 86 82 83 85 -64: 185 type=173 (RBDIHS) 80 82 86 87 -64: 186 type=173 (RBDIHS) 80 82 86 88 -64: 187 type=173 (RBDIHS) 83 82 86 87 -64: 188 type=173 (RBDIHS) 83 82 86 88 -64: 189 type=155 (RBDIHS) 69 89 91 92 -64: 190 type=156 (RBDIHS) 69 89 91 93 -64: 191 type=155 (RBDIHS) 90 89 91 92 -64: 192 type=157 (RBDIHS) 90 89 91 93 -64: 193 type=158 (RBDIHS) 89 91 93 95 -64: 194 type=159 (RBDIHS) 89 91 93 100 -64: 195 type=174 (RBDIHS) 91 93 95 98 -64: 196 type=175 (RBDIHS) 100 93 95 98 -64: 197 type=147 (RBDIHS) 91 93 95 96 -64: 198 type=147 (RBDIHS) 91 93 95 97 -64: 199 type=148 (RBDIHS) 94 93 95 96 -64: 200 type=148 (RBDIHS) 94 93 95 97 -64: 201 type=176 (RBDIHS) 94 93 95 98 -64: 202 type=149 (RBDIHS) 100 93 95 96 -64: 203 type=149 (RBDIHS) 100 93 95 97 -64: 204 type=150 (RBDIHS) 91 93 100 102 -64: 205 type=151 (RBDIHS) 95 93 100 102 -64: 206 type=177 (RBDIHS) 93 95 98 99 -64: 207 type=178 (RBDIHS) 96 95 98 99 -64: 208 type=178 (RBDIHS) 97 95 98 99 -64: 209 type=155 (RBDIHS) 93 100 102 103 -64: 210 type=156 (RBDIHS) 93 100 102 104 -64: 211 type=155 (RBDIHS) 101 100 102 103 -64: 212 type=157 (RBDIHS) 101 100 102 104 -64: 213 type=158 (RBDIHS) 100 102 104 106 -64: 214 type=159 (RBDIHS) 100 102 104 115 -64: 215 type=179 (RBDIHS) 102 104 106 109 -64: 216 type=180 (RBDIHS) 115 104 106 109 -64: 217 type=147 (RBDIHS) 102 104 106 107 -64: 218 type=147 (RBDIHS) 102 104 106 108 -64: 219 type=148 (RBDIHS) 105 104 106 107 -64: 220 type=148 (RBDIHS) 105 104 106 108 -64: 221 type=148 (RBDIHS) 105 104 106 109 -64: 222 type=149 (RBDIHS) 115 104 106 107 -64: 223 type=149 (RBDIHS) 115 104 106 108 -64: 224 type=150 (RBDIHS) 102 104 115 117 -64: 225 type=151 (RBDIHS) 106 104 115 117 -64: 226 type=148 (RBDIHS) 104 106 109 110 -64: 227 type=148 (RBDIHS) 104 106 109 111 -64: 228 type=181 (RBDIHS) 104 106 109 112 -64: 229 type=148 (RBDIHS) 107 106 109 110 -64: 230 type=148 (RBDIHS) 107 106 109 111 -64: 231 type=182 (RBDIHS) 107 106 109 112 -64: 232 type=148 (RBDIHS) 108 106 109 110 -64: 233 type=148 (RBDIHS) 108 106 109 111 -64: 234 type=182 (RBDIHS) 108 106 109 112 -64: 235 type=183 (RBDIHS) 106 109 112 113 -64: 236 type=183 (RBDIHS) 106 109 112 114 -64: 237 type=155 (RBDIHS) 104 115 117 118 -64: 238 type=156 (RBDIHS) 104 115 117 119 -64: 239 type=155 (RBDIHS) 116 115 117 118 -64: 240 type=157 (RBDIHS) 116 115 117 119 -64: 241 type=158 (RBDIHS) 115 117 119 121 -64: 242 type=159 (RBDIHS) 115 117 119 134 -64: 243 type=184 (RBDIHS) 117 119 121 124 -64: 244 type=185 (RBDIHS) 134 119 121 124 -64: 245 type=147 (RBDIHS) 117 119 121 122 -64: 246 type=147 (RBDIHS) 117 119 121 123 -64: 247 type=148 (RBDIHS) 120 119 121 122 -64: 248 type=148 (RBDIHS) 120 119 121 123 -64: 249 type=148 (RBDIHS) 120 119 121 124 -64: 250 type=149 (RBDIHS) 134 119 121 122 -64: 251 type=149 (RBDIHS) 134 119 121 123 -64: 252 type=150 (RBDIHS) 117 119 134 136 -64: 253 type=151 (RBDIHS) 121 119 134 136 -64: 254 type=148 (RBDIHS) 119 121 124 125 -64: 255 type=152 (RBDIHS) 119 121 124 126 -64: 256 type=152 (RBDIHS) 119 121 124 130 -64: 257 type=148 (RBDIHS) 122 121 124 125 -64: 258 type=148 (RBDIHS) 122 121 124 126 -64: 259 type=148 (RBDIHS) 122 121 124 130 -64: 260 type=148 (RBDIHS) 123 121 124 125 -64: 261 type=148 (RBDIHS) 123 121 124 126 -64: 262 type=148 (RBDIHS) 123 121 124 130 -64: 263 type=148 (RBDIHS) 121 124 126 127 -64: 264 type=148 (RBDIHS) 121 124 126 128 -64: 265 type=148 (RBDIHS) 121 124 126 129 -64: 266 type=148 (RBDIHS) 125 124 126 127 -64: 267 type=148 (RBDIHS) 125 124 126 128 -64: 268 type=148 (RBDIHS) 125 124 126 129 -64: 269 type=148 (RBDIHS) 130 124 126 127 -64: 270 type=148 (RBDIHS) 130 124 126 128 -64: 271 type=148 (RBDIHS) 130 124 126 129 -64: 272 type=148 (RBDIHS) 121 124 130 131 -64: 273 type=148 (RBDIHS) 121 124 130 132 -64: 274 type=148 (RBDIHS) 121 124 130 133 -64: 275 type=148 (RBDIHS) 125 124 130 131 -64: 276 type=148 (RBDIHS) 125 124 130 132 -64: 277 type=148 (RBDIHS) 125 124 130 133 -64: 278 type=148 (RBDIHS) 126 124 130 131 -64: 279 type=148 (RBDIHS) 126 124 130 132 -64: 280 type=148 (RBDIHS) 126 124 130 133 -64: 281 type=155 (RBDIHS) 119 134 136 137 -64: 282 type=156 (RBDIHS) 119 134 136 138 -64: 283 type=155 (RBDIHS) 135 134 136 137 -64: 284 type=157 (RBDIHS) 135 134 136 138 -64: 285 type=158 (RBDIHS) 134 136 138 140 -64: 286 type=159 (RBDIHS) 134 136 138 144 -64: 287 type=147 (RBDIHS) 136 138 140 141 -64: 288 type=147 (RBDIHS) 136 138 140 142 -64: 289 type=147 (RBDIHS) 136 138 140 143 -64: 290 type=148 (RBDIHS) 139 138 140 141 -64: 291 type=148 (RBDIHS) 139 138 140 142 -64: 292 type=148 (RBDIHS) 139 138 140 143 -64: 293 type=149 (RBDIHS) 144 138 140 141 -64: 294 type=149 (RBDIHS) 144 138 140 142 -64: 295 type=149 (RBDIHS) 144 138 140 143 -64: 296 type=150 (RBDIHS) 136 138 144 146 -64: 297 type=151 (RBDIHS) 140 138 144 146 -64: 298 type=155 (RBDIHS) 138 144 146 147 -64: 299 type=156 (RBDIHS) 138 144 146 148 -64: 300 type=155 (RBDIHS) 145 144 146 147 -64: 301 type=157 (RBDIHS) 145 144 146 148 -64: 302 type=158 (RBDIHS) 144 146 148 150 -64: 303 type=159 (RBDIHS) 144 146 148 154 -64: 304 type=147 (RBDIHS) 146 148 150 151 -64: 305 type=147 (RBDIHS) 146 148 150 152 -64: 306 type=147 (RBDIHS) 146 148 150 153 -64: 307 type=148 (RBDIHS) 149 148 150 151 -64: 308 type=148 (RBDIHS) 149 148 150 152 -64: 309 type=148 (RBDIHS) 149 148 150 153 -64: 310 type=149 (RBDIHS) 154 148 150 151 -64: 311 type=149 (RBDIHS) 154 148 150 152 -64: 312 type=149 (RBDIHS) 154 148 150 153 -64: Restr. Dih.: -64: nr: 0 -64: CBT Dih.: -64: nr: 0 -64: Fourier Dih.: -64: nr: 0 -64: Improper Dih.: -64: nr: 0 -64: Per. Imp. Dih.: -64: nr: 0 -64: Tab. Dih.: -64: nr: 0 -64: CMAP Dih.: -64: nr: 0 -64: GB 1-2 Pol.: -64: nr: 0 -64: GB 1-3 Pol.: -64: nr: 0 -64: GB 1-4 Pol.: -64: nr: 0 -64: GB Polariz.: -64: nr: 0 -64: Nonpolar Sol.: -64: nr: 0 -64: LJ-14: -64: nr: 1197 -64: iatoms: -64: 0 type=186 (LJ14) 0 7 -64: 1 type=186 (LJ14) 0 8 -64: 2 type=187 (LJ14) 0 9 -64: 3 type=188 (LJ14) 0 23 -64: 4 type=189 (LJ14) 0 24 -64: 5 type=190 (LJ14) 1 5 -64: 6 type=190 (LJ14) 1 6 -64: 7 type=190 (LJ14) 1 22 -64: 8 type=190 (LJ14) 2 5 -64: 9 type=190 (LJ14) 2 6 -64: 10 type=190 (LJ14) 2 22 -64: 11 type=190 (LJ14) 3 5 -64: 12 type=190 (LJ14) 3 6 -64: 13 type=190 (LJ14) 3 22 -64: 14 type=191 (LJ14) 4 10 -64: 15 type=191 (LJ14) 4 11 -64: 16 type=192 (LJ14) 4 12 -64: 17 type=190 (LJ14) 4 25 -64: 18 type=192 (LJ14) 4 26 -64: 19 type=193 (LJ14) 5 7 -64: 20 type=193 (LJ14) 5 8 -64: 21 type=191 (LJ14) 5 9 -64: 22 type=194 (LJ14) 5 23 -64: 23 type=186 (LJ14) 5 24 -64: 24 type=191 (LJ14) 6 13 -64: 25 type=191 (LJ14) 6 14 -64: 26 type=192 (LJ14) 6 15 -64: 27 type=195 (LJ14) 6 23 -64: 28 type=187 (LJ14) 6 24 -64: 29 type=193 (LJ14) 7 10 -64: 30 type=193 (LJ14) 7 11 -64: 31 type=191 (LJ14) 7 12 -64: 32 type=196 (LJ14) 7 22 -64: 33 type=193 (LJ14) 8 10 -64: 34 type=193 (LJ14) 8 11 -64: 35 type=191 (LJ14) 8 12 -64: 36 type=196 (LJ14) 8 22 -64: 37 type=191 (LJ14) 9 16 -64: 38 type=191 (LJ14) 9 17 -64: 39 type=187 (LJ14) 9 18 -64: 40 type=197 (LJ14) 9 22 -64: 41 type=193 (LJ14) 10 13 -64: 42 type=193 (LJ14) 10 14 -64: 43 type=191 (LJ14) 10 15 -64: 44 type=193 (LJ14) 11 13 -64: 45 type=193 (LJ14) 11 14 -64: 46 type=191 (LJ14) 11 15 -64: 47 type=190 (LJ14) 12 19 -64: 48 type=190 (LJ14) 12 20 -64: 49 type=190 (LJ14) 12 21 -64: 50 type=193 (LJ14) 13 16 -64: 51 type=193 (LJ14) 13 17 -64: 52 type=186 (LJ14) 13 18 -64: 53 type=193 (LJ14) 14 16 -64: 54 type=193 (LJ14) 14 17 -64: 55 type=186 (LJ14) 14 18 -64: 56 type=190 (LJ14) 16 19 -64: 57 type=190 (LJ14) 16 20 -64: 58 type=190 (LJ14) 16 21 -64: 59 type=190 (LJ14) 17 19 -64: 60 type=190 (LJ14) 17 20 -64: 61 type=190 (LJ14) 17 21 -64: 62 type=196 (LJ14) 22 27 -64: 63 type=197 (LJ14) 22 28 -64: 64 type=198 (LJ14) 22 38 -64: 65 type=190 (LJ14) 23 25 -64: 66 type=195 (LJ14) 23 26 -64: 67 type=186 (LJ14) 24 29 -64: 68 type=187 (LJ14) 24 30 -64: 69 type=187 (LJ14) 24 34 -64: 70 type=188 (LJ14) 24 39 -64: 71 type=189 (LJ14) 24 40 -64: 72 type=190 (LJ14) 25 27 -64: 73 type=190 (LJ14) 25 28 -64: 74 type=190 (LJ14) 25 38 -64: 75 type=191 (LJ14) 26 31 -64: 76 type=191 (LJ14) 26 32 -64: 77 type=191 (LJ14) 26 33 -64: 78 type=191 (LJ14) 26 35 -64: 79 type=191 (LJ14) 26 36 -64: 80 type=191 (LJ14) 26 37 -64: 81 type=190 (LJ14) 26 41 -64: 82 type=192 (LJ14) 26 42 -64: 83 type=193 (LJ14) 27 29 -64: 84 type=191 (LJ14) 27 30 -64: 85 type=191 (LJ14) 27 34 -64: 86 type=194 (LJ14) 27 39 -64: 87 type=186 (LJ14) 27 40 -64: 88 type=195 (LJ14) 28 39 -64: 89 type=187 (LJ14) 28 40 -64: 90 type=193 (LJ14) 29 31 -64: 91 type=193 (LJ14) 29 32 -64: 92 type=193 (LJ14) 29 33 -64: 93 type=193 (LJ14) 29 35 -64: 94 type=193 (LJ14) 29 36 -64: 95 type=193 (LJ14) 29 37 -64: 96 type=196 (LJ14) 29 38 -64: 97 type=191 (LJ14) 30 35 -64: 98 type=191 (LJ14) 30 36 -64: 99 type=191 (LJ14) 30 37 -64: 100 type=197 (LJ14) 30 38 -64: 101 type=191 (LJ14) 31 34 -64: 102 type=191 (LJ14) 32 34 -64: 103 type=191 (LJ14) 33 34 -64: 104 type=197 (LJ14) 34 38 -64: 105 type=196 (LJ14) 38 43 -64: 106 type=197 (LJ14) 38 44 -64: 107 type=198 (LJ14) 38 58 -64: 108 type=190 (LJ14) 39 41 -64: 109 type=195 (LJ14) 39 42 -64: 110 type=186 (LJ14) 40 45 -64: 111 type=186 (LJ14) 40 46 -64: 112 type=199 (LJ14) 40 47 -64: 113 type=188 (LJ14) 40 59 -64: 114 type=189 (LJ14) 40 60 -64: 115 type=190 (LJ14) 41 43 -64: 116 type=190 (LJ14) 41 44 -64: 117 type=190 (LJ14) 41 58 -64: 118 type=200 (LJ14) 42 48 -64: 119 type=200 (LJ14) 42 50 -64: 120 type=190 (LJ14) 42 61 -64: 121 type=192 (LJ14) 42 62 -64: 122 type=193 (LJ14) 43 45 -64: 123 type=193 (LJ14) 43 46 -64: 124 type=201 (LJ14) 43 47 -64: 125 type=194 (LJ14) 43 59 -64: 126 type=186 (LJ14) 43 60 -64: 127 type=202 (LJ14) 44 49 -64: 128 type=202 (LJ14) 44 51 -64: 129 type=200 (LJ14) 44 52 -64: 130 type=200 (LJ14) 44 54 -64: 131 type=195 (LJ14) 44 59 -64: 132 type=187 (LJ14) 44 60 -64: 133 type=201 (LJ14) 45 48 -64: 134 type=201 (LJ14) 45 50 -64: 135 type=196 (LJ14) 45 58 -64: 136 type=201 (LJ14) 46 48 -64: 137 type=201 (LJ14) 46 50 -64: 138 type=196 (LJ14) 46 58 -64: 139 type=203 (LJ14) 47 53 -64: 140 type=203 (LJ14) 47 55 -64: 141 type=204 (LJ14) 47 56 -64: 142 type=205 (LJ14) 47 58 -64: 143 type=203 (LJ14) 48 51 -64: 144 type=204 (LJ14) 48 54 -64: 145 type=203 (LJ14) 48 57 -64: 146 type=203 (LJ14) 49 50 -64: 147 type=206 (LJ14) 49 53 -64: 148 type=203 (LJ14) 49 56 -64: 149 type=204 (LJ14) 50 52 -64: 150 type=203 (LJ14) 50 57 -64: 151 type=206 (LJ14) 51 55 -64: 152 type=203 (LJ14) 51 56 -64: 153 type=203 (LJ14) 52 55 -64: 154 type=203 (LJ14) 53 54 -64: 155 type=206 (LJ14) 53 57 -64: 156 type=206 (LJ14) 55 57 -64: 157 type=196 (LJ14) 58 63 -64: 158 type=196 (LJ14) 58 64 -64: 159 type=198 (LJ14) 58 65 -64: 160 type=190 (LJ14) 59 61 -64: 161 type=195 (LJ14) 59 62 -64: 162 type=188 (LJ14) 60 66 -64: 163 type=189 (LJ14) 60 67 -64: 164 type=190 (LJ14) 61 63 -64: 165 type=190 (LJ14) 61 64 -64: 166 type=190 (LJ14) 61 65 -64: 167 type=190 (LJ14) 62 68 -64: 168 type=192 (LJ14) 62 69 -64: 169 type=194 (LJ14) 63 66 -64: 170 type=186 (LJ14) 63 67 -64: 171 type=194 (LJ14) 64 66 -64: 172 type=186 (LJ14) 64 67 -64: 173 type=196 (LJ14) 65 70 -64: 174 type=197 (LJ14) 65 71 -64: 175 type=198 (LJ14) 65 89 -64: 176 type=190 (LJ14) 66 68 -64: 177 type=195 (LJ14) 66 69 -64: 178 type=186 (LJ14) 67 72 -64: 179 type=186 (LJ14) 67 73 -64: 180 type=187 (LJ14) 67 74 -64: 181 type=188 (LJ14) 67 90 -64: 182 type=189 (LJ14) 67 91 -64: 183 type=190 (LJ14) 68 70 -64: 184 type=190 (LJ14) 68 71 -64: 185 type=190 (LJ14) 68 89 -64: 186 type=191 (LJ14) 69 75 -64: 187 type=191 (LJ14) 69 76 -64: 188 type=192 (LJ14) 69 77 -64: 189 type=190 (LJ14) 69 92 -64: 190 type=192 (LJ14) 69 93 -64: 191 type=193 (LJ14) 70 72 -64: 192 type=193 (LJ14) 70 73 -64: 193 type=191 (LJ14) 70 74 -64: 194 type=194 (LJ14) 70 90 -64: 195 type=186 (LJ14) 70 91 -64: 196 type=191 (LJ14) 71 78 -64: 197 type=191 (LJ14) 71 79 -64: 198 type=187 (LJ14) 71 80 -64: 199 type=195 (LJ14) 71 90 -64: 200 type=187 (LJ14) 71 91 -64: 201 type=193 (LJ14) 72 75 -64: 202 type=193 (LJ14) 72 76 -64: 203 type=191 (LJ14) 72 77 -64: 204 type=196 (LJ14) 72 89 -64: 205 type=193 (LJ14) 73 75 -64: 206 type=193 (LJ14) 73 76 -64: 207 type=191 (LJ14) 73 77 -64: 208 type=196 (LJ14) 73 89 -64: 209 type=190 (LJ14) 74 81 -64: 210 type=207 (LJ14) 74 82 -64: 211 type=197 (LJ14) 74 89 -64: 212 type=193 (LJ14) 75 78 -64: 213 type=193 (LJ14) 75 79 -64: 214 type=186 (LJ14) 75 80 -64: 215 type=193 (LJ14) 76 78 -64: 216 type=193 (LJ14) 76 79 -64: 217 type=186 (LJ14) 76 80 -64: 218 type=187 (LJ14) 77 83 -64: 219 type=187 (LJ14) 77 86 -64: 220 type=190 (LJ14) 78 81 -64: 221 type=208 (LJ14) 78 82 -64: 222 type=190 (LJ14) 79 81 -64: 223 type=208 (LJ14) 79 82 -64: 224 type=190 (LJ14) 80 84 -64: 225 type=190 (LJ14) 80 85 -64: 226 type=190 (LJ14) 80 87 -64: 227 type=190 (LJ14) 80 88 -64: 228 type=190 (LJ14) 81 83 -64: 229 type=190 (LJ14) 81 86 -64: 230 type=190 (LJ14) 83 87 -64: 231 type=190 (LJ14) 83 88 -64: 232 type=190 (LJ14) 84 86 -64: 233 type=190 (LJ14) 85 86 -64: 234 type=196 (LJ14) 89 94 -64: 235 type=197 (LJ14) 89 95 -64: 236 type=198 (LJ14) 89 100 -64: 237 type=190 (LJ14) 90 92 -64: 238 type=195 (LJ14) 90 93 -64: 239 type=186 (LJ14) 91 96 -64: 240 type=186 (LJ14) 91 97 -64: 241 type=209 (LJ14) 91 98 -64: 242 type=188 (LJ14) 91 101 -64: 243 type=189 (LJ14) 91 102 -64: 244 type=190 (LJ14) 92 94 -64: 245 type=190 (LJ14) 92 95 -64: 246 type=190 (LJ14) 92 100 -64: 247 type=190 (LJ14) 93 99 -64: 248 type=190 (LJ14) 93 103 -64: 249 type=192 (LJ14) 93 104 -64: 250 type=193 (LJ14) 94 96 -64: 251 type=193 (LJ14) 94 97 -64: 252 type=210 (LJ14) 94 98 -64: 253 type=194 (LJ14) 94 101 -64: 254 type=186 (LJ14) 94 102 -64: 255 type=195 (LJ14) 95 101 -64: 256 type=187 (LJ14) 95 102 -64: 257 type=190 (LJ14) 96 99 -64: 258 type=196 (LJ14) 96 100 -64: 259 type=190 (LJ14) 97 99 -64: 260 type=196 (LJ14) 97 100 -64: 261 type=211 (LJ14) 98 100 -64: 262 type=196 (LJ14) 100 105 -64: 263 type=197 (LJ14) 100 106 -64: 264 type=198 (LJ14) 100 115 -64: 265 type=190 (LJ14) 101 103 -64: 266 type=195 (LJ14) 101 104 -64: 267 type=186 (LJ14) 102 107 -64: 268 type=186 (LJ14) 102 108 -64: 269 type=187 (LJ14) 102 109 -64: 270 type=188 (LJ14) 102 116 -64: 271 type=189 (LJ14) 102 117 -64: 272 type=190 (LJ14) 103 105 -64: 273 type=190 (LJ14) 103 106 -64: 274 type=190 (LJ14) 103 115 -64: 275 type=191 (LJ14) 104 110 -64: 276 type=191 (LJ14) 104 111 -64: 277 type=197 (LJ14) 104 112 -64: 278 type=190 (LJ14) 104 118 -64: 279 type=192 (LJ14) 104 119 -64: 280 type=193 (LJ14) 105 107 -64: 281 type=193 (LJ14) 105 108 -64: 282 type=191 (LJ14) 105 109 -64: 283 type=194 (LJ14) 105 116 -64: 284 type=186 (LJ14) 105 117 -64: 285 type=195 (LJ14) 106 113 -64: 286 type=195 (LJ14) 106 114 -64: 287 type=195 (LJ14) 106 116 -64: 288 type=187 (LJ14) 106 117 -64: 289 type=193 (LJ14) 107 110 -64: 290 type=193 (LJ14) 107 111 -64: 291 type=196 (LJ14) 107 112 -64: 292 type=196 (LJ14) 107 115 -64: 293 type=193 (LJ14) 108 110 -64: 294 type=193 (LJ14) 108 111 -64: 295 type=196 (LJ14) 108 112 -64: 296 type=196 (LJ14) 108 115 -64: 297 type=197 (LJ14) 109 115 -64: 298 type=194 (LJ14) 110 113 -64: 299 type=194 (LJ14) 110 114 -64: 300 type=194 (LJ14) 111 113 -64: 301 type=194 (LJ14) 111 114 -64: 302 type=196 (LJ14) 115 120 -64: 303 type=197 (LJ14) 115 121 -64: 304 type=198 (LJ14) 115 134 -64: 305 type=190 (LJ14) 116 118 -64: 306 type=195 (LJ14) 116 119 -64: 307 type=186 (LJ14) 117 122 -64: 308 type=186 (LJ14) 117 123 -64: 309 type=187 (LJ14) 117 124 -64: 310 type=188 (LJ14) 117 135 -64: 311 type=189 (LJ14) 117 136 -64: 312 type=190 (LJ14) 118 120 -64: 313 type=190 (LJ14) 118 121 -64: 314 type=190 (LJ14) 118 134 -64: 315 type=191 (LJ14) 119 125 -64: 316 type=192 (LJ14) 119 126 -64: 317 type=192 (LJ14) 119 130 -64: 318 type=190 (LJ14) 119 137 -64: 319 type=192 (LJ14) 119 138 -64: 320 type=193 (LJ14) 120 122 -64: 321 type=193 (LJ14) 120 123 -64: 322 type=191 (LJ14) 120 124 -64: 323 type=194 (LJ14) 120 135 -64: 324 type=186 (LJ14) 120 136 -64: 325 type=191 (LJ14) 121 127 -64: 326 type=191 (LJ14) 121 128 -64: 327 type=191 (LJ14) 121 129 -64: 328 type=191 (LJ14) 121 131 -64: 329 type=191 (LJ14) 121 132 -64: 330 type=191 (LJ14) 121 133 -64: 331 type=195 (LJ14) 121 135 -64: 332 type=187 (LJ14) 121 136 -64: 333 type=193 (LJ14) 122 125 -64: 334 type=191 (LJ14) 122 126 -64: 335 type=191 (LJ14) 122 130 -64: 336 type=196 (LJ14) 122 134 -64: 337 type=193 (LJ14) 123 125 -64: 338 type=191 (LJ14) 123 126 -64: 339 type=191 (LJ14) 123 130 -64: 340 type=196 (LJ14) 123 134 -64: 341 type=197 (LJ14) 124 134 -64: 342 type=193 (LJ14) 125 127 -64: 343 type=193 (LJ14) 125 128 -64: 344 type=193 (LJ14) 125 129 -64: 345 type=193 (LJ14) 125 131 -64: 346 type=193 (LJ14) 125 132 -64: 347 type=193 (LJ14) 125 133 -64: 348 type=191 (LJ14) 126 131 -64: 349 type=191 (LJ14) 126 132 -64: 350 type=191 (LJ14) 126 133 -64: 351 type=191 (LJ14) 127 130 -64: 352 type=191 (LJ14) 128 130 -64: 353 type=191 (LJ14) 129 130 -64: 354 type=196 (LJ14) 134 139 -64: 355 type=197 (LJ14) 134 140 -64: 356 type=198 (LJ14) 134 144 -64: 357 type=190 (LJ14) 135 137 -64: 358 type=195 (LJ14) 135 138 -64: 359 type=186 (LJ14) 136 141 -64: 360 type=186 (LJ14) 136 142 -64: 361 type=186 (LJ14) 136 143 -64: 362 type=188 (LJ14) 136 145 -64: 363 type=189 (LJ14) 136 146 -64: 364 type=190 (LJ14) 137 139 -64: 365 type=190 (LJ14) 137 140 -64: 366 type=190 (LJ14) 137 144 -64: 367 type=190 (LJ14) 138 147 -64: 368 type=192 (LJ14) 138 148 -64: 369 type=193 (LJ14) 139 141 -64: 370 type=193 (LJ14) 139 142 -64: 371 type=193 (LJ14) 139 143 -64: 372 type=194 (LJ14) 139 145 -64: 373 type=186 (LJ14) 139 146 -64: 374 type=195 (LJ14) 140 145 -64: 375 type=187 (LJ14) 140 146 -64: 376 type=196 (LJ14) 141 144 -64: 377 type=196 (LJ14) 142 144 -64: 378 type=196 (LJ14) 143 144 -64: 379 type=196 (LJ14) 144 149 -64: 380 type=197 (LJ14) 144 150 -64: 381 type=198 (LJ14) 144 154 -64: 382 type=190 (LJ14) 145 147 -64: 383 type=195 (LJ14) 145 148 -64: 384 type=186 (LJ14) 146 151 -64: 385 type=186 (LJ14) 146 152 -64: 386 type=186 (LJ14) 146 153 -64: 387 type=188 (LJ14) 146 155 -64: 388 type=190 (LJ14) 147 149 -64: 389 type=190 (LJ14) 147 150 -64: 390 type=190 (LJ14) 147 154 -64: 391 type=193 (LJ14) 149 151 -64: 392 type=193 (LJ14) 149 152 -64: 393 type=193 (LJ14) 149 153 -64: 394 type=194 (LJ14) 149 155 -64: 395 type=195 (LJ14) 150 155 -64: 396 type=196 (LJ14) 151 154 -64: 397 type=196 (LJ14) 152 154 -64: 398 type=196 (LJ14) 153 154 -64: Coulomb-14: -64: nr: 0 -64: LJC-14 q: -64: nr: 0 -64: LJC Pairs NB: -64: nr: 0 -64: LJ (SR): -64: nr: 0 -64: Buck.ham (SR): -64: nr: 0 -64: LJ: -64: nr: 0 -64: B.ham: -64: nr: 0 -64: Disper. corr.: -64: nr: 0 -64: Coulomb (SR): -64: nr: 0 -64: Coul: -64: nr: 0 -64: RF excl.: -64: nr: 0 -64: Coul. recip.: -64: nr: 0 -64: LJ recip.: -64: nr: 0 -64: DPD: -64: nr: 0 -64: Polarization: -64: nr: 0 -64: Water Pol.: -64: nr: 0 -64: Thole Pol.: -64: nr: 0 -64: Anharm. Pol.: -64: nr: 0 -64: Position Rest.: -64: nr: 0 -64: Flat-b. P-R.: -64: nr: 0 -64: Dis. Rest.: -64: nr: 0 -64: D.R.Viol. (nm): -64: nr: 0 -64: Orient. Rest.: -64: nr: 0 -64: Ori. R. RMSD: -64: nr: 0 -64: Angle Rest.: -64: nr: 0 -64: Angle Rest. Z: -64: nr: 0 -64: Dih. Rest.: -64: nr: 0 -64: Dih. Rest. Vi.: -64: nr: 0 -64: Constraint: -64: nr: 0 -64: Constr. No Co.: -64: nr: 0 -64: Settle: -64: nr: 0 -64: Virtual site 1: -64: nr: 0 -64: Virtual site 2: -64: nr: 0 -64: Virt. site 2fd: -64: nr: 0 -64: Virtual site 3: -64: nr: 0 -64: Virt. site 3fd: -64: nr: 0 -64: Vir. site 3fad: -64: nr: 0 -64: Vir. site 3out: -64: nr: 0 -64: Virt. site 4fd: -64: nr: 0 -64: Vir. site 4fdn: -64: nr: 0 -64: Virtual site N: -64: nr: 0 -64: COM Pull En.: -64: nr: 0 -64: Dens. fitting: -64: nr: 0 -64: Quantum En.: -64: nr: 0 -64: NN Potential: -64: nr: 0 -64: Potential: -64: nr: 0 -64: Kinetic En.: -64: nr: 0 -64: Total Energy: -64: nr: 0 -64: Conserved En.: -64: nr: 0 -64: Temperature: -64: nr: 0 -64: Vir. Temp.: -64: nr: 0 -64: Pres. DC: -64: nr: 0 -64: Pressure: -64: nr: 0 -64: dH/dl constr.: -64: nr: 0 -64: dVremain/dl: -64: nr: 0 -64: dEkin/dl: -64: nr: 0 -64: dVcoul/dl: -64: nr: 0 -64: dVvdw/dl: -64: nr: 0 -64: dVbonded/dl: -64: nr: 0 -64: dVrestraint/dl: -64: nr: 0 -64: dVtemp/dl: -64: nr: 0 -64: grp[T-Coupling ] nr=1, name=[ rest] -64: grp[Energy Mon. ] nr=1, name=[ rest] -64: grp[Acc. not used] nr=1, name=[ rest] -64: grp[Freeze ] nr=1, name=[ rest] -64: grp[User1 ] nr=1, name=[ rest] -64: grp[User2 ] nr=1, name=[ rest] -64: grp[VCM ] nr=1, name=[ rest] -64: grp[Compressed X] nr=1, name=[ rest] -64: grp[Or. Res. Fit] nr=1, name=[ rest] -64: grp[QMMM ] nr=1, name=[ rest] -64: grpname (11): -64: grpname[0]={name="System"} -64: grpname[1]={name="Protein"} -64: grpname[2]={name="Protein-H"} -64: grpname[3]={name="C-alpha"} -64: grpname[4]={name="Backbone"} -64: grpname[5]={name="MainChain"} -64: grpname[6]={name="MainChain+Cb"} -64: grpname[7]={name="MainChain+H"} -64: grpname[8]={name="SideChain"} -64: grpname[9]={name="SideChain-H"} -64: grpname[10]={name="rest"} -64: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM -64: allocated 0 0 0 0 0 0 0 0 0 0 -64: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 -64: box (3x3): -64: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} -64: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} -64: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} -64: box_rel (3x3): -64: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: boxv (3x3): -64: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: pres_prev (3x3): -64: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: svir_prev (3x3): -64: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: fvir_prev (3x3): -64: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: nosehoover_xi: not available -64: x (156x3): -64: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} -64: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} -64: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} -64: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} -64: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} -64: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} -64: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} -64: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} -64: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} -64: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} -64: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} -64: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} -64: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} -64: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} -64: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} -64: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} -64: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} -64: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} -64: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} -64: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} -64: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} -64: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} -64: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} -64: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} -64: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} -64: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} -64: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} -64: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} -64: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} -64: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} -64: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} -64: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} -64: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} -64: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} -64: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} -64: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} -64: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} -64: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} -64: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} -64: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} -64: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} -64: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} -64: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} -64: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} -64: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} -64: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} -64: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} -64: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} -64: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} -64: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} -64: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} -64: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} -64: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} -64: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} -64: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} -64: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} -64: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} -64: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} -64: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} -64: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} -64: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} -64: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} -64: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} -64: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} -64: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} -64: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} -64: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} -64: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} -64: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} -64: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} -64: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} -64: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} -64: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} -64: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} -64: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} -64: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} -64: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} -64: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} -64: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} -64: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} -64: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} -64: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} -64: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} -64: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} -64: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} -64: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} -64: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} -64: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} -64: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} -64: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} -64: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} -64: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} -64: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} -64: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} -64: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} -64: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} -64: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} -64: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} -64: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} -64: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} -64: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} -64: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} -64: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} -64: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} -64: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} -64: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} -64: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} -64: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} -64: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} -64: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} -64: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} -64: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} -64: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} -64: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} -64: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} -64: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} -64: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} -64: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} -64: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} -64: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} -64: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} -64: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} -64: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} -64: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} -64: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} -64: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} -64: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} -64: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} -64: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} -64: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} -64: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} -64: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} -64: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} -64: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} -64: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} -64: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} -64: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} -64: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} -64: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} -64: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} -64: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} -64: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} -64: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} -64: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} -64: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} -64: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} -64: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} -64: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} -64: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} -64: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} -64: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} -64: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} -64: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} -64: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} -64: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} -64: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} -64: v (156x3): -64: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} -64: Group statistics -64: T-Coupling : 156 (total 156 atoms) -64: Energy Mon. : 156 (total 156 atoms) -64: Acc. not used: 156 (total 156 atoms) -64: Freeze : 156 (total 156 atoms) -64: User1 : 156 (total 156 atoms) -64: User2 : 156 (total 156 atoms) -64: VCM : 156 (total 156 atoms) -64: Compressed X: 156 (total 156 atoms) -64: Or. Res. Fit: 156 (total 156 atoms) -64: QMMM : 156 (total 156 atoms) -64: [ OK ] DumpTest.WorksWithTpr (7 ms) -64: [ RUN ] DumpTest.WorksWithTprAndMdpWriting -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) -64: [----------] 2 tests from DumpTest (8 ms total) -64: -64: [----------] 3 tests from HelpwritingTest -64: [ RUN ] HelpwritingTest.ConvertTprWritesHelp -64: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) -64: [ RUN ] HelpwritingTest.DumpWritesHelp -64: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) -64: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp -64: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) -64: [----------] 3 tests from HelpwritingTest (0 ms total) -64: -64: [----------] 7 tests from GmxMakeNdx -64: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups -64: -64: Reading structure file -64: Going to read 0 old index file(s) -64: Analysing residue names: -64: There are: 16 Protein residues -64: Analysing Protein... -64: -64: 0 System : 256 atoms -64: 1 Protein : 256 atoms -64: 2 Protein-H : 139 atoms -64: 3 C-alpha : 16 atoms -64: 4 Backbone : 48 atoms -64: 5 MainChain : 63 atoms -64: 6 MainChain+Cb : 78 atoms -64: 7 MainChain+H : 81 atoms -64: 8 SideChain : 175 atoms -64: 9 SideChain-H : 76 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (2 ms) -64: [ RUN ] GmxMakeNdx.HandlesNoStructureInput -64: Going to read 1 old index file(s) -64: Deducing 22 atoms in the system from indices in the index file -64: -64: 0 System : 22 atoms -64: 1 Protein : 22 atoms -64: 2 Protein-H : 10 atoms -64: 3 C-alpha : 1 atoms -64: 4 Backbone : 5 atoms -64: 5 MainChain : 7 atoms -64: 6 MainChain+Cb : 8 atoms -64: 7 MainChain+H : 9 atoms -64: 8 SideChain : 13 atoms -64: 9 SideChain-H : 3 atoms -64: 10 CA : 1 atoms -64: 11 C_&_r_1 : 1 atoms -64: 12 C_&_r_2 : 1 atoms -64: 13 N_&_r_2 : 1 atoms -64: 14 N_&_r_3 : 1 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: Copied index group 1 'Protein' -64: Copied index group 2 'Protein-H' -64: Merged two groups with OR: 22 10 -> 22 -64: -64: > -64: [ OK ] GmxMakeNdx.HandlesNoStructureInput (1 ms) -64: [ RUN ] GmxMakeNdx.HandlesNotProtein -64: Going to read 1 old index file(s) -64: Deducing 6 atoms in the system from indices in the index file -64: -64: 0 System : 6 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) -64: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult -64: Going to read 1 old index file(s) -64: Deducing 22 atoms in the system from indices in the index file -64: -64: 0 System : 22 atoms -64: 1 Protein : 22 atoms -64: 2 Protein-H : 10 atoms -64: 3 C-alpha : 1 atoms -64: 4 Backbone : 5 atoms -64: 5 MainChain : 7 atoms -64: 6 MainChain+Cb : 8 atoms -64: 7 MainChain+H : 9 atoms -64: 8 SideChain : 13 atoms -64: 9 SideChain-H : 3 atoms -64: 10 CA : 1 atoms -64: 11 C_&_r_1 : 1 atoms -64: 12 C_&_r_2 : 1 atoms -64: 13 N_&_r_2 : 1 atoms -64: 14 N_&_r_3 : 1 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: Copied index group 4 'Backbone' -64: Copied index group 8 'SideChain' -64: Merged two groups with AND: 5 13 -> 0 -64: Group is empty -64: -64: > -64: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) -64: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile -64: Going to read 1 old index file(s) -64: Deducing 6 atoms in the system from indices in the index file -64: -64: 0 System : 6 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: Removed group 0 'System' -64: -64: > -64: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) -64: [ RUN ] GmxMakeNdx.Splitres -64: -64: Reading structure file -64: Going to read 0 old index file(s) -64: Analysing residue names: -64: There are: 2 Water residues -64: -64: 0 System : 6 atoms -64: 1 Water : 6 atoms -64: 2 SOL : 6 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: Splitting group 1 'Water' into residues -64: -64: > -64: [ OK ] GmxMakeNdx.Splitres (0 ms) -64: [ RUN ] GmxMakeNdx.Splitat -64: -64: Reading structure file -64: Going to read 0 old index file(s) -64: Analysing residue names: -64: There are: 2 Water residues -64: -64: 0 System : 6 atoms -64: 1 Water : 6 atoms -64: 2 SOL : 6 atoms -64: -64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups -64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues -64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help -64: 'r': residue 'res' nr 'chain' char -64: "name": group 'case': case sensitive 'q': save and quit -64: 'ri': residue index -64: -64: > -64: Splitting group 1 'Water' into atoms -64: -64: > -64: [ OK ] GmxMakeNdx.Splitat (0 ms) -64: [----------] 7 tests from GmxMakeNdx (7 ms total) -64: -64: [----------] 4 tests from ReportMethodsTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Setting the LD random seed to -843060490 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated -64: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) -64: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted -64: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) -64: [ RUN ] ReportMethodsTest.WritesCorrectInformation -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) -64: [ RUN ] ReportMethodsTest.ToolEndToEndTest -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: section: Methods -64: subsection: Simulation system -64: A system of 1 molecules (156 atoms) was simulated. -64: -64: subsection: Simulation settings -64: A total of 0 ns were simulated with a time step of 1 fs. -64: Neighbor searching was performed every 10 steps. -64: The Cut-off algorithm was used for electrostatic interactions. -64: with a cut-off of 1 nm. -64: A single cut-off of 1.1 nm was used for Van der Waals interactions. -64: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) -64: [----------] 4 tests from ReportMethodsTest (1 ms total) -64: -64: [----------] 4 tests from ConvertTprTest -64: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting the LD random seed to 1979546582 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: Input file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 0 -64: Runtime for the run 0 ps -64: Run end step 0 -64: Run end time 0 ps -64: -64: Extending remaining runtime by 100 ps -64: -64: Output file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 100000 -64: Runtime for the run 100 ps -64: Run end step 100000 -64: Run end time 100 ps -64: -64: Input file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 100000 -64: Runtime for the run 100 ps -64: Run end step 100000 -64: Run end time 100 ps -64: -64: Extending remaining runtime by 100 ps -64: -64: Output file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 200000 -64: Runtime for the run 200 ps -64: Run end step 200000 -64: Run end time 200 ps -64: -64: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (231 ms) -64: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting the LD random seed to -671367441 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: Input file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 0 -64: Runtime for the run 0 ps -64: Run end step 0 -64: Run end time 0 ps -64: -64: Extending remaining runtime to 100 ps -64: -64: Output file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 100000 -64: Runtime for the run 100 ps -64: Run end step 100000 -64: Run end time 100 ps -64: -64: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (231 ms) -64: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting nsteps to 102 -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting the LD random seed to -604002562 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: Input file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 0 -64: Runtime for the run 0 ps -64: Run end step 0 -64: Run end time 0 ps -64: -64: -64: Output file: -64: Run start step 0 -64: Run start time 0 ps -64: Step to be made during run 102 -64: Runtime for the run 0.102 ps -64: Run end step 102 -64: Run end time 0.102 ps -64: -64: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (232 ms) -64: [ RUN ] ConvertTprTest.generateVelocitiesTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -64: NVE simulation with an initial temperature of zero: will use a Verlet -64: buffer of 10%. Check your energy drift! -64: -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting the LD random seed to 2050998268 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: -64: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: [ OK ] ConvertTprTest.generateVelocitiesTest (230 ms) -64: [----------] 4 tests from ConvertTprTest (926 ms total) -64: -64: [----------] 1 test from ConvertTprNoVelocityTest -64: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest -64: -64: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -64: For a correct single-point energy evaluation with nsteps = 0, use -64: continuation = yes to avoid constraining the input coordinates. -64: -64: Generating 1-4 interactions: fudge = 0.5 -64: -64: NOTE 2 [file lysozyme.top, line 1465]: -64: System has non-zero total charge: 2.000000 -64: Total charge should normally be an integer. See -64: https://manual.gromacs.org/current/user-guide/floating-point.html -64: for discussion on how close it should be to an integer. -64: -64: -64: -64: -64: NOTE 3 [file lysozyme.top, line 1465]: -64: Zero-step energy minimization will alter the coordinates before -64: calculating the energy. If you just want the energy of a single point, -64: try zero-step MD (with unconstrained_start = yes). To do multiple -64: single-point energy evaluations of different configurations of the same -64: topology, use mdrun -rerun. -64: -64: Number of degrees of freedom in T-Coupling group rest is 465.00 -64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -64: -64: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: -64: You are using a plain Coulomb cut-off, which might produce artifacts. -64: You might want to consider using PME electrostatics. -64: -64: -64: -64: There were 4 NOTEs -64: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -64: Setting the LD random seed to -356515841 -64: -64: Generated 330891 of the 330891 non-bonded parameter combinations -64: -64: Generated 330891 of the 330891 1-4 parameter combinations -64: -64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -64: Analysing residue names: -64: There are: 10 Protein residues -64: Analysing Protein... -64: -64: This run will generate roughly 0 Mb of data -64: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (230 ms) -64: [----------] 1 test from ConvertTprNoVelocityTest (230 ms total) -64: -64: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: trr version: GMX_trn_file (single precision) -64: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (1 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (1 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) -64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 -64: Will write trr: Trajectory in portable xdr format -64: Group 0 ( System) has 6 elements -64: Group 1 (FirstWaterMolecule) has 3 elements -64: Group 2 (SecondWaterMolecule) has 3 elements -64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -64: -> frame 1 time 1.000 -64: Last written: frame 1 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: Select group for output -64: Selected 2: 'SecondWaterMolecule' -64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) -64: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (11 ms total) -64: -64: [----------] 30 tests from Works/TrjconvDumpTest -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (4 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (1 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. -64: Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 -64: Precision of /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) -64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms -64: Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 0 ps -64: -> frame 0 time 0.000 -64: Last written: frame 0 time 0.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) -64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 -64: Will write trr: Trajectory in portable xdr format -64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 -64: -64: Dumping frame at t= 1 ps -64: -> frame 0 time 1.000 -64: Last written: frame 0 time 1.000 -64: -64: -64: Note that major changes are planned in future for trjconv, to improve usability and utility. -64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) -64: [----------] 30 tests from Works/TrjconvDumpTest (24 ms total) -64: -64: [----------] Global test environment tear-down -64: [==========] 63 tests from 8 test suites ran. (1671 ms total) -64: [ PASSED ] 63 tests. -64/96 Test #64: ToolUnitTests ................................ Passed 1.87 sec -test 65 - Start 65: ToolWithLeaksUnitTests - -65: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/ToolWithLeaksUnitTests.xml" -65: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests -65: Test timeout computed to be: 1920 -65: [==========] Running 2 tests from 2 test suites. -65: [----------] Global test environment set-up. -65: [----------] 1 test from ConvertTprTest -65: [ RUN ] ConvertTprTest.selectIndexTest -65: -65: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -65: For a correct single-point energy evaluation with nsteps = 0, use -65: continuation = yes to avoid constraining the input coordinates. -65: -65: Generating 1-4 interactions: fudge = 0.5 -65: -65: NOTE 2 [file lysozyme.top, line 1465]: -65: System has non-zero total charge: 2.000000 -65: Total charge should normally be an integer. See -65: https://manual.gromacs.org/current/user-guide/floating-point.html -65: for discussion on how close it should be to an integer. -65: -65: -65: -65: Number of degrees of freedom in T-Coupling group rest is 465.00 -65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -65: -65: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -65: NVE simulation with an initial temperature of zero: will use a Verlet -65: buffer of 10%. Check your energy drift! -65: -65: -65: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: -65: You are using a plain Coulomb cut-off, which might produce artifacts. -65: You might want to consider using PME electrostatics. -65: -65: -65: -65: There were 4 NOTEs -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Group 0 ( System) has 156 elements -65: Group 1 ( Protein) has 156 elements -65: Group 2 ( Protein-H) has 75 elements -65: Group 3 ( C-alpha) has 10 elements -65: Group 4 ( Backbone) has 30 elements -65: Group 5 ( MainChain) has 40 elements -65: Group 6 ( MainChain+Cb) has 49 elements -65: Group 7 ( MainChain+H) has 52 elements -65: Group 8 ( SideChain) has 104 elements -65: Group 9 ( SideChain-H) has 35 elements -65: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -65: Reduced ilist BONDS from 156 to 75 entries -65: Reduced ilist ANGLES from 281 to 98 entries -65: Reduced ilist PDIHS from 29 to 12 entries -65: Reduced ilist RBDIHS from 313 to 89 entries -65: Reduced ilist LJ14 from 399 to 107 entries -65: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Setting the LD random seed to -134482478 -65: -65: Generated 330891 of the 330891 non-bonded parameter combinations -65: -65: Generated 330891 of the 330891 1-4 parameter combinations -65: -65: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -65: -65: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero -65: Analysing residue names: -65: There are: 10 Protein residues -65: Analysing Protein... -65: -65: This run will generate roughly 0 Mb of data -65: Selected 2: 'Protein-H' -65: [ OK ] ConvertTprTest.selectIndexTest (238 ms) -65: [----------] 1 test from ConvertTprTest (238 ms total) -65: -65: [----------] 1 test from ConvertTprNoVelocityTest -65: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity -65: -65: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -65: For a correct single-point energy evaluation with nsteps = 0, use -65: continuation = yes to avoid constraining the input coordinates. -65: -65: Generating 1-4 interactions: fudge = 0.5 -65: -65: NOTE 2 [file lysozyme.top, line 1465]: -65: System has non-zero total charge: 2.000000 -65: Total charge should normally be an integer. See -65: https://manual.gromacs.org/current/user-guide/floating-point.html -65: for discussion on how close it should be to an integer. -65: -65: -65: -65: -65: NOTE 3 [file lysozyme.top, line 1465]: -65: Zero-step energy minimization will alter the coordinates before -65: calculating the energy. If you just want the energy of a single point, -65: try zero-step MD (with unconstrained_start = yes). To do multiple -65: single-point energy evaluations of different configurations of the same -65: topology, use mdrun -rerun. -65: -65: Number of degrees of freedom in T-Coupling group rest is 465.00 -65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -65: -65: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: -65: You are using a plain Coulomb cut-off, which might produce artifacts. -65: You might want to consider using PME electrostatics. -65: -65: -65: -65: There were 4 NOTEs -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Group 0 ( System) has 156 elements -65: Group 1 ( Protein) has 156 elements -65: Group 2 ( Protein-H) has 75 elements -65: Group 3 ( C-alpha) has 10 elements -65: Group 4 ( Backbone) has 30 elements -65: Group 5 ( MainChain) has 40 elements -65: Group 6 ( MainChain+Cb) has 49 elements -65: Group 7 ( MainChain+H) has 52 elements -65: Group 8 ( SideChain) has 104 elements -65: Group 9 ( SideChain-H) has 35 elements -65: Select a group: Will write subset Protein-H of original tpx containing 75 atoms -65: Reduced ilist BONDS from 156 to 75 entries -65: Reduced ilist ANGLES from 281 to 98 entries -65: Reduced ilist PDIHS from 29 to 12 entries -65: Reduced ilist RBDIHS from 313 to 89 entries -65: Reduced ilist LJ14 from 399 to 107 entries -65: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries -65: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -65: Setting the LD random seed to -285409431 -65: -65: Generated 330891 of the 330891 non-bonded parameter combinations -65: -65: Generated 330891 of the 330891 1-4 parameter combinations -65: -65: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' -65: Analysing residue names: -65: There are: 10 Protein residues -65: Analysing Protein... -65: -65: This run will generate roughly 0 Mb of data -65: Selected 2: 'Protein-H' -65: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (224 ms) -65: [----------] 1 test from ConvertTprNoVelocityTest (224 ms total) -65: -65: [----------] Global test environment tear-down -65: [==========] 2 tests from 2 test suites ran. (463 ms total) -65: [ PASSED ] 2 tests. -65/96 Test #65: ToolWithLeaksUnitTests ....................... Passed 0.66 sec -test 66 - Start 66: FileIOTests - -66: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/FileIOTests.xml" -66: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/fileio/tests -66: Test timeout computed to be: 30 -66: [==========] Running 421 tests from 17 test suites. -66: [----------] Global test environment set-up. -66: [----------] 4 tests from Checkpoint -66: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent -66: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) -66: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent -66: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) -66: [ RUN ] Checkpoint.KvtRoundTripInt64 -66: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) -66: [ RUN ] Checkpoint.KvtRoundTripReal -66: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) -66: [----------] 4 tests from Checkpoint (0 ms total) -66: -66: [----------] 1 test from StructureIOTest -66: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids -66: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) -66: [----------] 1 test from StructureIOTest (0 ms total) -66: -66: [----------] 2 tests from FileMD5Test -66: [ RUN ] FileMD5Test.CanComputeMD5 -66: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) -66: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong -66: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) -66: [----------] 2 tests from FileMD5Test (1 ms total) -66: -66: [----------] 4 tests from FileTypeTest -66: [ RUN ] FileTypeTest.CorrectValueForEmptyString -66: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) -66: [ RUN ] FileTypeTest.CorrectValueForNoExtension -66: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) -66: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension -66: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) -66: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters -66: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) -66: [----------] 4 tests from FileTypeTest (0 ms total) -66: -66: [----------] 4 tests from ColorMapTest -66: [ RUN ] ColorMapTest.CanReadFromFile -66: [ OK ] ColorMapTest.CanReadFromFile (0 ms) -66: [ RUN ] ColorMapTest.CanWriteToFile -66: [ OK ] ColorMapTest.CanWriteToFile (0 ms) -66: [ RUN ] ColorMapTest.RoundTrip -66: [ OK ] ColorMapTest.RoundTrip (0 ms) -66: [ RUN ] ColorMapTest.SearchWorks -66: [ OK ] ColorMapTest.SearchWorks (0 ms) -66: [----------] 4 tests from ColorMapTest (0 ms total) -66: -66: [----------] 4 tests from MatioTest -66: [ RUN ] MatioTest.CanWriteToFile -66: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) -66: [ RUN ] MatioTest.CanConvertToExistingRealMatrix -66: Converted a 4x3 matrix with 4 levels to reals -66: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) -66: [ RUN ] MatioTest.CanConvertToNewRealMatrix -66: Converted a 4x3 matrix with 4 levels to reals -66: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) -66: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting -66: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) -66: [----------] 4 tests from MatioTest (1 ms total) -66: -66: [----------] 3 tests from MrcSerializer -66: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet -66: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) -66: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize -66: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) -66: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip -66: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) -66: [----------] 3 tests from MrcSerializer (0 ms total) -66: -66: [----------] 4 tests from MrcDensityMap -66: [ RUN ] MrcDensityMap.RoundTripIsIdempotent -66: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) -66: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent -66: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) -66: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile -66: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) -66: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile -66: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) -66: [----------] 4 tests from MrcDensityMap (1 ms total) -66: -66: [----------] 8 tests from MrcDensityMapHeaderTest -66: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader -66: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect -66: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid -66: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven -66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined -66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues -66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents -66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) -66: [ RUN ] MrcDensityMapHeaderTest.IsSane -66: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) -66: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) -66: -66: [----------] 10 tests from ReadTest -66: [ RUN ] ReadTest.get_eint_ReadsInteger -66: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) -66: [ RUN ] ReadTest.get_eint_WarnsAboutFloat -66: -66: ERROR 1 [file unknown]: -66: Right hand side '0.8' for parameter 'test' in parameter file is not an -66: integer value -66: -66: -66: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) -66: [ RUN ] ReadTest.get_eint_WarnsAboutString -66: -66: ERROR 1 [file unknown]: -66: Right hand side 'hello' for parameter 'test' in parameter file is not an -66: integer value -66: -66: -66: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) -66: [ RUN ] ReadTest.get_eint64_ReadsInteger -66: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) -66: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat -66: -66: ERROR 1 [file unknown]: -66: Right hand side '0.8' for parameter 'test' in parameter file is not an -66: integer value -66: -66: -66: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) -66: [ RUN ] ReadTest.get_eint64_WarnsAboutString -66: -66: ERROR 1 [file unknown]: -66: Right hand side 'hello' for parameter 'test' in parameter file is not an -66: integer value -66: -66: -66: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) -66: [ RUN ] ReadTest.get_ereal_ReadsInteger -66: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) -66: [ RUN ] ReadTest.get_ereal_ReadsFloat -66: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) -66: [ RUN ] ReadTest.get_ereal_WarnsAboutString -66: -66: ERROR 1 [file unknown]: -66: Right hand side 'hello' for parameter 'test' in parameter file is not a -66: real value -66: -66: -66: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) -66: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString -66: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) -66: [----------] 10 tests from ReadTest (0 ms total) -66: -66: [----------] 3 tests from TimeControlTest -66: [ RUN ] TimeControlTest.UnSetHasNoValue -66: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) -66: [ RUN ] TimeControlTest.CanSetValue -66: [ OK ] TimeControlTest.CanSetValue (0 ms) -66: [ RUN ] TimeControlTest.CanUnsetValueAgain -66: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) -66: [----------] 3 tests from TimeControlTest (0 ms total) -66: -66: [----------] 1 test from FileIOXdrSerializerTest -66: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect -66: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) -66: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) -66: -66: [----------] 1 test from TngTest -66: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal -66: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) -66: [----------] 1 test from TngTest (0 ms total) -66: -66: [----------] 4 tests from XvgioTest -66: [ RUN ] XvgioTest.readXvgIntWorks -66: [ OK ] XvgioTest.readXvgIntWorks (0 ms) -66: [ RUN ] XvgioTest.readXvgRealWorks -66: [ OK ] XvgioTest.readXvgRealWorks (0 ms) -66: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks -66: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) -66: [ RUN ] XvgioTest.readXvgDeprecatedWorks -66: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) -66: [----------] 4 tests from XvgioTest (0 ms total) -66: -66: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest -66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 -66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) -66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 -66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) -66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 -66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) -66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 -66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) -66: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (1 ms total) -66: -66: [----------] 360 tests from FileTypeMatch/FileTypeTest -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) -66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 -66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) -66: [----------] 360 tests from FileTypeMatch/FileTypeTest (2 ms total) -66: -66: [----------] 4 tests from XvgReadTimeSeries/XvgioTest -66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 -66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) -66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 -66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) -66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 -66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) -66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 -66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) -66: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (1 ms total) -66: -66: [----------] Global test environment tear-down -66: [==========] 421 tests from 17 test suites ran. (12 ms total) -66: [ PASSED ] 421 tests. -66/96 Test #66: FileIOTests .................................. Passed 0.21 sec -test 67 - Start 67: SelectionUnitTests - -67: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/SelectionUnitTests.xml" -67: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection/tests -67: Test timeout computed to be: 30 -67: [==========] Running 201 tests from 11 test suites. -67: [----------] Global test environment set-up. -67: [----------] 1 test from IndexGroupTest -67: [ RUN ] IndexGroupTest.RemovesDuplicates -67: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) -67: [----------] 1 test from IndexGroupTest (0 ms total) -67: -67: [----------] 15 tests from IndexBlockTest -67: [ RUN ] IndexBlockTest.CreatesUnknownBlock -67: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) -67: [ RUN ] IndexBlockTest.CreatesAtomBlock -67: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) -67: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology -67: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) -67: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology -67: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) -67: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology -67: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) -67: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology -67: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) -67: [ RUN ] IndexBlockTest.CreatesSingleBlock -67: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive -67: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) -67: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive -67: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative -67: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial -67: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive -67: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative -67: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive -67: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) -67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative -67: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) -67: [----------] 15 tests from IndexBlockTest (1 ms total) -67: -67: [----------] 11 tests from IndexMapTest -67: [ RUN ] IndexMapTest.InitializesAtomBlock -67: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) -67: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom -67: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) -67: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle -67: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) -67: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue -67: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) -67: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule -67: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) -67: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll -67: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) -67: [ RUN ] IndexMapTest.InitializesMoleculeBlock -67: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) -67: [ RUN ] IndexMapTest.MapsSingleBlock -67: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) -67: [ RUN ] IndexMapTest.MapsResidueBlocks -67: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) -67: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask -67: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) -67: [ RUN ] IndexMapTest.HandlesMultipleRequests -67: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) -67: [----------] 11 tests from IndexMapTest (2 ms total) -67: -67: [----------] 3 tests from IndexGroupsAndNamesTest -67: [ RUN ] IndexGroupsAndNamesTest.containsNames -67: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) -67: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing -67: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) -67: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect -67: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) -67: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) -67: -67: [----------] 15 tests from NeighborhoodSearchTest -67: [ RUN ] NeighborhoodSearchTest.SimpleSearch -67: [ OK ] NeighborhoodSearchTest.SimpleSearch (9 ms) -67: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY -67: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (9 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearchBox -67: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic -67: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (5 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC -67: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC -67: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox -67: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) -67: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch -67: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch -67: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (24 ms) -67: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches -67: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) -67: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC -67: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) -67: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC -67: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) -67: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs -67: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) -67: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions -67: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) -67: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions -67: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) -67: [----------] 15 tests from NeighborhoodSearchTest (57 ms total) -67: -67: [----------] 13 tests from PositionCalculationTest -67: [ RUN ] PositionCalculationTest.ComputesAtomPositions -67: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex -67: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions -67: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions -67: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions -67: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions -67: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole -67: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax -67: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) -67: [ RUN ] PositionCalculationTest.ComputesPositionMask -67: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) -67: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms -67: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) -67: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 -67: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) -67: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations -67: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) -67: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations -67: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) -67: [----------] 13 tests from PositionCalculationTest (3 ms total) -67: -67: [----------] 33 tests from SelectionCollectionTest -67: [ RUN ] SelectionCollectionTest.HandlesNoSelections -67: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType -67: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests -67: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry -67: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) -67: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile -67: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace -67: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions -67: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue -67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 -67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 -67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 -67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 -67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 -67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 -67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference -67: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed -67: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup -67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed -67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 -67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo -67: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes -67: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo -67: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation -67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 -67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) -67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 -67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets -67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 -67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 -67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) -67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 -67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) -67: [ RUN ] SelectionCollectionTest.RetrieveValidSelection -67: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) -67: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection -67: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) -67: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection -67: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) -67: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately -67: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) -67: [----------] 33 tests from SelectionCollectionTest (9 ms total) -67: -67: [----------] 14 tests from SelectionCollectionInteractiveTest -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput -67: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation -67: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput -67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput -67: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups -67: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections -67: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus -67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus -67: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus -67: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline -67: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections -67: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine -67: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput -67: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) -67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively -67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) -67: [----------] 14 tests from SelectionCollectionInteractiveTest (4 ms total) -67: -67: [----------] 70 tests from SelectionCollectionDataTest -67: [ RUN ] SelectionCollectionDataTest.HandlesAllNone -67: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr -67: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesResnr -67: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesResIndex -67: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex -67: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesAtomname -67: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname -67: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype -67: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesChain -67: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesMass -67: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesCharge -67: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc -67: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode -67: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy -67: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesBeta -67: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesResname -67: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords -67: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue -67: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName -67: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords -67: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword -67: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword -67: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword -67: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword -67: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier -67: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier -67: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier -67: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) -67: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges -67: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) -67: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology -67: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets -67: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames -67: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections -67: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed -67: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections -67: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed -67: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions -67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers -67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions -67: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges -67: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges -67: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode -67: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching -67: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching -67: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean -67: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters -67: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions -67: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame -67: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords -67: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods -67: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions -67: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic -67: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons -67: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions -67: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables -67: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables -67: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables -67: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier -67: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable -67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables -67: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis -67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables -67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables -67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables -67: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups -67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups -67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) -67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 -67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) -67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation -67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) -67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation -67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) -67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent -67: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) -67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation -67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) -67: [----------] 70 tests from SelectionCollectionDataTest (40 ms total) -67: -67: [----------] 17 tests from SelectionOptionTest -67: [ RUN ] SelectionOptionTest.ParsesSimpleSelection -67: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired -67: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired -67: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) -67: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired -67: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) -67: [ RUN ] SelectionOptionTest.ChecksEmptySelections -67: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) -67: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections -67: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesTooManySelections -67: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesTooFewSelections -67: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText -67: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesAdjuster -67: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster -67: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster -67: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster -67: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection -67: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections -67: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection -67: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) -67: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster -67: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) -67: [----------] 17 tests from SelectionOptionTest (4 ms total) -67: -67: [----------] 9 tests from SelectionFileOptionTest -67: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile -67: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions -67: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) -67: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile -67: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile -67: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet -67: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) -67: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile -67: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile -67: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile -67: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) -67: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles -67: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) -67: [----------] 9 tests from SelectionFileOptionTest (2 ms total) -67: -67: [----------] Global test environment tear-down -67: [==========] 201 tests from 11 test suites ran. (127 ms total) -67: [ PASSED ] 201 tests. -67/96 Test #67: SelectionUnitTests ........................... Passed 0.39 sec -test 68 - Start 68: MdrunOutputTests - -68: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunOutputTests.xml" -68: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -68: Test timeout computed to be: 600 -68: [==========] Running 12 tests from 5 test suites. -68: [----------] Global test environment set-up. -68: [----------] 1 test from MdrunTest -68: [ RUN ] MdrunTest.WritesHelp -68: [ OK ] MdrunTest.WritesHelp (36 ms) -68: [----------] 1 test from MdrunTest (36 ms total) -68: -68: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput -68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group rest is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to 2013253607 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.008 198.7 -68: (ns/day) (hour/ns) -68: Performance: 20.811 1.153 -68: Reading frame 0 time 0.000 -68: # Atoms 6 -68: Reading frame 1 time 0.001 Last frame 1 time 0.001 -68: -68: -68: Item #frames Timestep (ps) -68: Step 2 0.001 -68: Time 2 0.001 -68: Lambda 0 -68: Coords 2 0.001 -68: Velocities 0 -68: Forces 0 -68: Box 2 0.001 -68: Checking file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc -68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (14 ms) -68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group rest is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to -101761025 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.021 0.010 199.0 -68: (ns/day) (hour/ns) -68: Performance: 16.504 1.454 -68: Reading frame 0 time 0.000 -68: # Atoms 6 -68: Reading frame 1 time 0.001 Last frame 1 time 0.001 -68: -68: -68: Item #frames Timestep (ps) -68: Step 2 0.001 -68: Time 2 0.001 -68: Lambda 0 -68: Coords 2 0.001 -68: Velocities 0 -68: Forces 0 -68: Box 2 0.001 -68: Checking file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc -68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (15 ms) -68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 -68: Generating 1-4 interactions: fudge = 0.5 -68: Number of degrees of freedom in T-Coupling group rest is 9.00 -68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -68: NVE simulation: will use the initial temperature of 2573.591 K for -68: determining the Verlet buffer size -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There were 2 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc2' -68: 1 steps, 0.0 ps. -68: Setting the LD random seed to 2136997631 -68: -68: Generated 3 of the 3 non-bonded parameter combinations -68: -68: Generated 3 of the 3 1-4 parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.022 0.011 199.1 -68: (ns/day) (hour/ns) -68: Performance: 15.705 1.528 -68: Reading frame 0 time 0.000 -68: # Atoms 3 -68: Reading frame 1 time 0.001 Last frame 1 time 0.001 -68: -68: -68: Item #frames Timestep (ps) -68: Step 2 0.001 -68: Time 2 0.001 -68: Lambda 0 -68: Coords 2 0.001 -68: Velocities 0 -68: Forces 0 -68: Box 2 0.001 -68: Checking file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc -68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (18 ms) -68: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (48 ms total) -68: -68: [----------] 2 tests from Argon12/OutputFiles -68: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.008 198.7 -68: (ns/day) (hour/ns) -68: Performance: 191.210 0.126 -68: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (12 ms) -68: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -68: that with the Verlet scheme, nstlist has no effect on the accuracy of -68: your simulation. -68: -68: -68: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -68: Setting nstcalcenergy (100) equal to nstenergy (4) -68: -68: Number of degrees of freedom in T-Coupling group System is 33.00 -68: -68: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: -68: NVE simulation: will use the initial temperature of 68.810 K for -68: determining the Verlet buffer size -68: -68: -68: There were 3 NOTEs -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Can not increase nstlist because an NVE ensemble is used -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'Argon' -68: 16 steps, 0.0 ps. -68: Generated 1 of the 1 non-bonded parameter combinations -68: -68: Excluding 1 bonded neighbours molecule type 'Argon' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -68: -68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -68: -68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.007 198.4 -68: (ns/day) (hour/ns) -68: Performance: 199.514 0.120 -68: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (12 ms) -68: [----------] 2 tests from Argon12/OutputFiles (25 ms total) -68: -68: [----------] 3 tests from MdrunCanWrite/Trajectories -68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 6 steps, 0.0 ps. -68: Setting the LD random seed to -303563319 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.017 0.009 199.0 -68: (ns/day) (hour/ns) -68: Performance: 70.961 0.338 -68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (16 ms) -68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 6 steps, 0.0 ps. -68: Setting the LD random seed to -340955297 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.018 0.009 199.0 -68: (ns/day) (hour/ns) -68: Performance: 68.195 0.352 -68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (15 ms) -68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 6 steps, 0.0 ps. -68: Setting the LD random seed to -810044034 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.015 0.008 199.0 -68: (ns/day) (hour/ns) -68: Performance: 78.917 0.304 -68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (15 ms) -68: [----------] 3 tests from MdrunCanWrite/Trajectories (46 ms total) -68: -68: [----------] 3 tests from MdrunCanWrite/NptTrajectories -68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -374477336 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.010 0.005 198.6 -68: (ns/day) (hour/ns) -68: Performance: 52.047 0.461 -68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (12 ms) -68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 -68: -68: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -68: The Berendsen barostat does not generate any strictly correct ensemble, -68: and should not be used for new production simulations (in our opinion). -68: We recommend using the C-rescale barostat instead. -68: -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: -68: There was 1 WARNING -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -306184841 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.012 0.006 198.5 -68: (ns/day) (hour/ns) -68: Performance: 44.490 0.539 -68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (11 ms) -68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 -68: Number of degrees of freedom in T-Coupling group System is 12.00 -68: -68: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: -68: You are using a plain Coulomb cut-off, which might produce artifacts. -68: You might want to consider using PME electrostatics. -68: -68: -68: -68: There was 1 NOTE -68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -68: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 -68: -68: Using 1 MPI process -68: Using 2 OpenMP threads -68: -68: -68: NOTE: The number of threads is not equal to the number of (logical) cpus -68: and the -pin option is set to auto: will not pin threads to cpus. -68: This can lead to significant performance degradation. -68: Consider using -pin on (and -pinoffset in case you run multiple jobs). -68: starting mdrun 'spc-and-methanol' -68: 2 steps, 0.0 ps. -68: Setting the LD random seed to -1646469457 -68: -68: Generated 8 of the 10 non-bonded parameter combinations -68: -68: Excluding 2 bonded neighbours molecule type 'Methanol' -68: -68: Excluding 2 bonded neighbours molecule type 'SOL' -68: -68: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -68: -68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -68: -68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -68: -68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -68: -68: Note that mdrun will redetermine rlist based on the actual pair-list setup -68: -68: This run will generate roughly 0 Mb of data -68: -68: Writing final coordinates. -68: -68: Core t (s) Wall t (s) (%) -68: Time: 0.013 0.006 198.4 -68: (ns/day) (hour/ns) -68: Performance: 40.438 0.594 -68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (11 ms) -68: [----------] 3 tests from MdrunCanWrite/NptTrajectories (35 ms total) -68: -68: [----------] Global test environment tear-down -68: [==========] 12 tests from 5 test suites ran. (313 ms total) -68: [ PASSED ] 12 tests. -68/96 Test #68: MdrunOutputTests ............................. Passed 0.51 sec -test 69 - Start 69: MdrunModulesTests - -69: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunModulesTests.xml" -69: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -69: Test timeout computed to be: 600 -69: [==========] Running 15 tests from 3 test suites. -69: [----------] Global test environment set-up. -69: [----------] 9 tests from DensityFittingTest -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 2 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 3 steps. -69: Potential Energy = -3.8565254e+03 -69: Maximum force = 4.5099883e+03 on atom 3 -69: Norm of force = 1.6816849e+03 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -42091009 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (6 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 2 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 3 steps. -69: Potential Energy = -9.8207725e+03 -69: Maximum force = 7.3954834e+03 on atom 2 -69: Norm of force = 2.7825089e+03 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -402981381 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (5 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Overriding nsteps with value passed on the command line: 4 steps -69: -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 4 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 5 steps. -69: Potential Energy = -5.4739302e+03 -69: Maximum force = 6.1322041e+03 on atom 2 -69: Norm of force = 1.7702155e+03 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1342327558 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (5 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 2 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 3 steps. -69: Potential Energy = -3.8565254e+03 -69: Maximum force = 4.5099883e+03 on atom 3 -69: Norm of force = 1.6816849e+03 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1996488703 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (4 ms) -69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 2 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 3 steps. -69: Potential Energy = -2.7138664e+04 -69: Maximum force = 6.7827656e+03 on atom 2 -69: Norm of force = 1.9608866e+03 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 607116733 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (4 ms) -69: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch -69: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) -69: [ RUN ] DensityFittingTest.CheckpointWorks -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -69: Setting nstcalcenergy (100) equal to nstenergy (2) -69: -69: Number of degrees of freedom in T-Coupling group rest is 33.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: -69: NVE simulation: will use the initial temperature of 68.810 K for -69: determining the Verlet buffer size -69: -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Argon' -69: 2 steps, 0.0 ps. -69: Setting the LD random seed to -12583490 -69: -69: Generated 1 of the 1 non-bonded parameter combinations -69: -69: Excluding 1 bonded neighbours molecule type 'Argon' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K -69: -69: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.015 0.008 198.7 -69: (ns/day) (hour/ns) -69: Performance: 34.515 0.695 -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps -69: Can not increase nstlist because an NVE ensemble is used -69: -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting mdrun 'Argon' -69: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.009 0.004 197.9 -69: (ns/day) (hour/ns) -69: Performance: 99.628 0.241 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (19 ms) -69: [----------] 9 tests from DensityFittingTest (46 ms total) -69: -69: [----------] 4 tests from MimicTest -69: [ RUN ] MimicTest.OneQuantumMol -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 21.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -69: -69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 19 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 184.1 -69: (ns/day) (hour/ns) -69: Performance: 299.494 0.080 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1620100105 -69: -69: Generated 10 of the 10 non-bonded parameter combinations -69: -69: Generated 10 of the 10 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] MimicTest.OneQuantumMol (6 ms) -69: [ RUN ] MimicTest.AllQuantumMol -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 21.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -69: -69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 27 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.000 0.000 185.0 -69: (ns/day) (hour/ns) -69: Performance: 335.234 0.072 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1945884331 -69: -69: Generated 10 of the 10 non-bonded parameter combinations -69: -69: Generated 10 of the 10 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] MimicTest.AllQuantumMol (4 ms) -69: [ RUN ] MimicTest.TwoQuantumMol -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 21.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -69: NVE simulation with an initial temperature of zero: will use a Verlet -69: buffer of 10%. Check your energy drift! -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -69: -69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 23 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.000 0.000 184.4 -69: (ns/day) (hour/ns) -69: Performance: 367.906 0.065 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -872958017 -69: -69: Generated 10 of the 10 non-bonded parameter combinations -69: -69: Generated 10 of the 10 1-4 parameter combinations -69: -69: Excluding 2 bonded neighbours molecule type 'SOL' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] MimicTest.TwoQuantumMol (5 ms) -69: [ RUN ] MimicTest.BondCuts -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -69: For a correct single-point energy evaluation with nsteps = 0, use -69: continuation = yes to avoid constraining the input coordinates. -69: -69: Generating 1-4 interactions: fudge = 0.5 -69: Number of degrees of freedom in T-Coupling group rest is 66.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -69: NVE simulation: will use the initial temperature of 300.368 K for -69: determining the Verlet buffer size -69: -69: -69: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 3 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Can not increase nstlist because an NVE ensemble is used -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -69: Reading frame 0 time 0.000 Last frame 0 time 0.000 -69: -69: NOTE: 24 % of the run time was spent in pair search, -69: you might want to increase nstlist (this has no effect on accuracy) -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.001 0.000 190.1 -69: (ns/day) (hour/ns) -69: Performance: 216.480 0.111 -69: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file -69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1292898321 -69: -69: Generated 2211 of the 2211 non-bonded parameter combinations -69: -69: Generated 2211 of the 2211 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -69: -69: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] MimicTest.BondCuts (10 ms) -69: [----------] 4 tests from MimicTest (27 ms total) -69: -69: [----------] 2 tests from WithIntegrator/ImdTest -69: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 -69: Generating 1-4 interactions: fudge = 1 -69: -69: NOTE 1 [file glycine_vacuo.top, line 12]: -69: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an -69: estimated oscillational period of 1.0e-02 ps, which is less than 10 times -69: the time step of 2.0e-03 ps. -69: Maybe you forgot to change the constraints mdp option. -69: -69: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -69: Number of degrees of freedom in T-Coupling group System is 27.00 -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 -69: -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: IMD: Enabled. This simulation will accept incoming IMD connections. -69: IMD: Pulling from IMD remote is enabled (-imdpull). -69: IMD: Setting port for connection requests to 0. -69: IMD: Setting up incoming socket. -69: IMD: Listening for IMD connection on port 42165. -69: IMD: -imdwait not set, starting simulation. -69: starting mdrun 'Glycine' -69: 2 steps, 0.0 ps. -69: Setting the LD random seed to 2133752715 -69: -69: Generated 20503 of the 20503 non-bonded parameter combinations -69: -69: Generated 17396 of the 20503 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Glycine' -69: -69: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero -69: -69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -69: -69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -69: -69: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm -69: -69: Note that mdrun will redetermine rlist based on the actual pair-list setup -69: -69: This run will generate roughly 0 Mb of data -69: -69: Writing final coordinates. -69: -69: Core t (s) Wall t (s) (%) -69: Time: 0.018 0.009 199.0 -69: (ns/day) (hour/ns) -69: Performance: 57.434 0.418 -69: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (68 ms) -69: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 -69: -69: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -69: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not -69: apply to steep. -69: -69: Generating 1-4 interactions: fudge = 1 -69: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). -69: Number of degrees of freedom in T-Coupling group System is 27.00 -69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -69: -69: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: -69: You are using a plain Coulomb cut-off, which might produce artifacts. -69: You might want to consider using PME electrostatics. -69: -69: -69: -69: There were 2 NOTEs -69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -69: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -69: Using 1 MPI process -69: Using 2 OpenMP threads -69: -69: -69: NOTE: The number of threads is not equal to the number of (logical) cpus -69: and the -pin option is set to auto: will not pin threads to cpus. -69: This can lead to significant performance degradation. -69: Consider using -pin on (and -pinoffset in case you run multiple jobs). -69: -69: IMD: Enabled. This simulation will accept incoming IMD connections. -69: IMD: Pulling from IMD remote is enabled (-imdpull). -69: IMD: Setting port for connection requests to 0. -69: IMD: Setting up incoming socket. -69: IMD: Listening for IMD connection on port 49449. -69: IMD: -imdwait not set, starting simulation. -69: -69: Steepest Descents: -69: Tolerance (Fmax) = 1.00000e+01 -69: Number of steps = 2 -69: -69: Energy minimization reached the maximum number of steps before the forces -69: reached the requested precision Fmax < 10. -69: -69: writing lowest energy coordinates. -69: -69: Steepest Descents did not converge to Fmax < 10 in 3 steps. -69: Potential Energy = 1.1977064e+03 -69: Maximum force = 1.7794877e+04 on atom 9 -69: Norm of force = 7.8732901e+03 -69: Setting the LD random seed to -1358987337 -69: -69: Generated 20503 of the 20503 non-bonded parameter combinations -69: -69: Generated 17396 of the 20503 1-4 parameter combinations -69: -69: Excluding 3 bonded neighbours molecule type 'Glycine' -69: -69: This run will generate roughly 0 Mb of data -69: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (59 ms) -69: [----------] 2 tests from WithIntegrator/ImdTest (127 ms total) -69: -69: [----------] Global test environment tear-down -69: [==========] 15 tests from 3 test suites ran. (315 ms total) -69: [ PASSED ] 15 tests. -69/96 Test #69: MdrunModulesTests ............................ Passed 0.52 sec -test 70 - Start 70: MdrunIOTests - -70: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunIOTests.xml" -70: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -70: Test timeout computed to be: 600 -70: [==========] Running 76 tests from 13 test suites. -70: [----------] Global test environment set-up. -70: [----------] 9 tests from GromppTest -70: [ RUN ] GromppTest.EmptyMdpFileWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Number of degrees of freedom in T-Coupling group rest is 12.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -70: NVE simulation: will use the initial temperature of 1046.791 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Setting the LD random seed to -1889639521 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] GromppTest.EmptyMdpFileWorks (4 ms) -70: [ RUN ] GromppTest.SimulatedAnnealingWorks -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Simulated annealing for group rest: Periodic, 4 timepoints -70: Time (ps) Temperature (K) -70: 0.0 298.0 -70: 2.0 320.0 -70: 4.0 320.0 -70: 6.0 298.0 -70: Number of degrees of freedom in T-Coupling group rest is 12.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -70: NVE simulation: will use the initial temperature of 1046.791 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Setting the LD random seed to -553906209 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] GromppTest.SimulatedAnnealingWorks (3 ms) -70: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Simulated annealing for group Methanol: Single, 3 timepoints -70: Time (ps) Temperature (K) -70: 0.0 298.0 -70: 3.0 280.0 -70: 6.0- 270.0 -70: Simulated annealing for group SOL: Periodic, 4 timepoints -70: Time (ps) Temperature (K) -70: 0.0 298.0 -70: 2.0 320.0 -70: 4.0 320.0 -70: 6.0 298.0 -70: Number of degrees of freedom in T-Coupling group Methanol is 7.20 -70: Number of degrees of freedom in T-Coupling group SOL is 4.80 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -70: NVE simulation: will use the initial temperature of 1046.791 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Setting the LD random seed to -415238534 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (3 ms) -70: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError -70: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) -70: [ RUN ] GromppTest.HandlesMaxwarn -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: -70: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -70: The Berendsen thermostat does not generate the correct kinetic energy -70: distribution, and should not be used for new production simulations (in -70: our opinion). We would recommend the V-rescale thermostat. -70: -70: Number of degrees of freedom in T-Coupling group System is 12.00 -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: -70: There was 1 WARNING -70: Setting the LD random seed to -1082429451 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] GromppTest.HandlesMaxwarn (2 ms) -70: [ RUN ] GromppTest.MaxwarnShouldBePositive -70: [ OK ] GromppTest.MaxwarnShouldBePositive (1 ms) -70: [ RUN ] GromppTest.ValidTransformationCoord -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Pull group 1 'SOL' has 3 atoms -70: Pull group 2 'Methanol' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 12.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -70: NVE simulation: will use the initial temperature of 1046.791 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 5 -70: 2 3 2 0.613 nm 0.000 nm -70: 1 3 5 -70: 2 3 2 0.613 nm 0.000 nm -70: -70: There were 3 NOTEs -70: Setting the LD random seed to -201354531 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: [ OK ] GromppTest.ValidTransformationCoord (3 ms) -70: [ RUN ] GromppTest.InvalidTransformationCoord -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -70: For a correct single-point energy evaluation with nsteps = 0, use -70: continuation = yes to avoid constraining the input coordinates. -70: -70: Pull group 1 'SOL' has 3 atoms -70: Pull group 2 'Methanol' has 3 atoms -70: Number of degrees of freedom in T-Coupling group rest is 12.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -70: NVE simulation: will use the initial temperature of 1046.791 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 5 -70: 2 3 2 0.613 nm 0.000 nm -70: 1 3 5 -70: 2 3 2 Setting the LD random seed to -537056005 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) -70: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic -70: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) -70: [----------] 9 tests from GromppTest (22 ms total) -70: -70: [----------] 6 tests from MdrunTerminationTest -70: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to -1401684490 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.1 -70: (ns/day) (hour/ns) -70: Performance: 42.323 0.567 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 4 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 2 -70: Runtime for the run 0.002 ps -70: Run end step 2 -70: Run end time 0.002 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.005 0.003 196.7 -70: (ns/day) (hour/ns) -70: Performance: 98.075 0.245 -70: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (17 ms) -70: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 1, rlist from 1.032 to 1 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 100 steps, 0.1 ps. -70: -70: Step 6: Run time exceeded 0.000 hours, will terminate the run within 200 steps -70: Setting the LD random seed to 834591680 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.037 0.019 199.3 -70: (ns/day) (hour/ns) -70: Performance: 468.681 0.051 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 102 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 100 -70: Runtime for the run 0.1 ps -70: Run end step 100 -70: Run end time 0.1 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 102 -70: Runtime for the run 0.102 ps -70: Run end step 102 -70: Run end time 0.102 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.006 0.003 197.0 -70: (ns/day) (hour/ns) -70: Performance: 90.131 0.266 -70: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (29 ms) -70: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to 1593831101 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.3 -70: (ns/day) (hour/ns) -70: Performance: 43.070 0.557 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 4 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 2 -70: Runtime for the run 0.002 ps -70: Run end step 2 -70: Run end time 0.002 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.009 0.004 198.7 -70: (ns/day) (hour/ns) -70: Performance: 60.455 0.397 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 6 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 6 -70: Runtime for the run 0.006 ps -70: Run end step 6 -70: Run end time 0.006 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 199.1 -70: (ns/day) (hour/ns) -70: Performance: 44.660 0.537 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 8 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 6 -70: Runtime for the run 0.006 ps -70: Run end step 6 -70: Run end time 0.006 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 8 -70: Runtime for the run 0.008 ps -70: Run end step 8 -70: Run end time 0.008 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.009 0.005 198.8 -70: (ns/day) (hour/ns) -70: Performance: 56.576 0.424 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: NOTE: 28 % of the run time was spent in pair search, -70: you might want to increase nstlist (this has no effect on accuracy) -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.000 0.000 168.3 -70: (ns/day) (hour/ns) -70: Performance: 517.697 0.046 -70: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (36 ms) -70: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to -9455617 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.010 0.005 198.2 -70: (ns/day) (hour/ns) -70: Performance: 53.107 0.452 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 4 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps. -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 2 -70: Runtime for the run 0.002 ps -70: Run end step 2 -70: Run end time 0.002 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.008 0.004 198.0 -70: (ns/day) (hour/ns) -70: Performance: 100.949 0.238 -70: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (17 ms) -70: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to -1354826817 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.008 0.004 197.9 -70: (ns/day) (hour/ns) -70: Performance: 62.769 0.382 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 4 -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 2 -70: Runtime for the run 0.002 ps -70: Run end step 2 -70: Run end time 0.002 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (9 ms) -70: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There was 1 NOTE -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 2 steps, 0.0 ps. -70: Setting the LD random seed to -34750497 -70: -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.008 0.004 197.8 -70: (ns/day) (hour/ns) -70: Performance: 65.370 0.367 -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Setting nsteps to 4 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -70: Input file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 2 -70: Runtime for the run 0.002 ps -70: Run end step 2 -70: Run end time 0.002 ps -70: -70: -70: Output file: -70: Run start step 0 -70: Run start time 0 ps -70: Step to be made during run 4 -70: Runtime for the run 0.004 ps -70: Run end step 4 -70: Run end time 0.004 ps -70: -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.008 0.004 198.7 -70: (ns/day) (hour/ns) -70: Performance: 67.664 0.355 -70: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (14 ms) -70: [----------] 6 tests from MdrunTerminationTest (124 ms total) -70: -70: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks -70: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 198.4 -70: (ns/day) (hour/ns) -70: Performance: 216.495 0.111 -70: trr version: GMX_trn_file (single precision) -70: -70: -70: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (12 ms) -70: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.005 198.9 -70: (ns/day) (hour/ns) -70: Performance: 271.823 0.088 -70: -70: -70: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (10 ms) -70: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (22 ms total) -70: -70: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 198.6 -70: (ns/day) (hour/ns) -70: Performance: 200.808 0.120 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.006 199.0 -70: (ns/day) (hour/ns) -70: Performance: 120.886 0.199 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.3 -70: (ns/day) (hour/ns) -70: Performance: 128.380 0.187 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (30 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.9 -70: (ns/day) (hour/ns) -70: Performance: 243.060 0.099 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.005 198.3 -70: (ns/day) (hour/ns) -70: Performance: 142.051 0.169 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 198.7 -70: (ns/day) (hour/ns) -70: Performance: 114.688 0.209 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (29 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 199.3 -70: (ns/day) (hour/ns) -70: Performance: 244.594 0.098 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 199.6 -70: (ns/day) (hour/ns) -70: Performance: 72.347 0.332 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 199.1 -70: (ns/day) (hour/ns) -70: Performance: 99.994 0.240 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (35 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 199.1 -70: (ns/day) (hour/ns) -70: Performance: 208.304 0.115 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 100.175 0.240 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 198.8 -70: (ns/day) (hour/ns) -70: Performance: 114.458 0.210 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (32 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.5 -70: (ns/day) (hour/ns) -70: Performance: 252.825 0.095 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 199.1 -70: (ns/day) (hour/ns) -70: Performance: 119.560 0.201 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 199.2 -70: (ns/day) (hour/ns) -70: Performance: 105.996 0.226 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (30 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 198.7 -70: (ns/day) (hour/ns) -70: Performance: 220.929 0.109 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 199.1 -70: (ns/day) (hour/ns) -70: Performance: 114.394 0.210 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.0 -70: (ns/day) (hour/ns) -70: Performance: 91.085 0.263 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (32 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.664 0.332 200.0 -70: (ns/day) (hour/ns) -70: Performance: 4.424 5.425 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.299 0.149 199.9 -70: (ns/day) (hour/ns) -70: Performance: 5.208 4.608 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 199.2 -70: (ns/day) (hour/ns) -70: Performance: 109.996 0.218 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (500 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.5 -70: (ns/day) (hour/ns) -70: Performance: 246.759 0.097 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 199.1 -70: (ns/day) (hour/ns) -70: Performance: 124.020 0.194 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.4 -70: (ns/day) (hour/ns) -70: Performance: 76.061 0.316 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (34 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.2 -70: (ns/day) (hour/ns) -70: Performance: 176.274 0.136 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 82.147 0.292 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 82.500 0.291 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (39 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 198.9 -70: (ns/day) (hour/ns) -70: Performance: 170.654 0.141 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 85.462 0.281 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.2 -70: (ns/day) (hour/ns) -70: Performance: 92.237 0.260 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (44 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.5 -70: (ns/day) (hour/ns) -70: Performance: 131.353 0.183 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.6 -70: (ns/day) (hour/ns) -70: Performance: 85.192 0.282 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.3 -70: (ns/day) (hour/ns) -70: Performance: 71.912 0.334 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (44 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 199.5 -70: (ns/day) (hour/ns) -70: Performance: 138.662 0.173 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 199.5 -70: (ns/day) (hour/ns) -70: Performance: 106.941 0.224 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.3 -70: (ns/day) (hour/ns) -70: Performance: 76.581 0.313 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (44 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 170.224 0.141 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 83.819 0.286 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.2 -70: (ns/day) (hour/ns) -70: Performance: 90.824 0.264 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (42 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.009 199.4 -70: (ns/day) (hour/ns) -70: Performance: 157.838 0.152 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.2 -70: (ns/day) (hour/ns) -70: Performance: 95.179 0.252 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 199.3 -70: (ns/day) (hour/ns) -70: Performance: 79.757 0.301 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (41 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 174.462 0.138 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 100.505 0.239 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 87.873 0.273 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (38 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.9 -70: (ns/day) (hour/ns) -70: Performance: 188.024 0.128 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.4 -70: (ns/day) (hour/ns) -70: Performance: 90.019 0.267 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 91.638 0.262 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (45 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 199.0 -70: (ns/day) (hour/ns) -70: Performance: 154.069 0.156 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.0 -70: (ns/day) (hour/ns) -70: Performance: 93.734 0.256 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.023 0.011 199.2 -70: (ns/day) (hour/ns) -70: Performance: 68.356 0.351 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (57 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.9 -70: (ns/day) (hour/ns) -70: Performance: 182.126 0.132 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.0 -70: (ns/day) (hour/ns) -70: Performance: 95.527 0.251 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.5 -70: (ns/day) (hour/ns) -70: Performance: 96.028 0.250 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (50 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 199.1 -70: (ns/day) (hour/ns) -70: Performance: 138.524 0.173 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.6 -70: (ns/day) (hour/ns) -70: Performance: 130.528 0.184 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.025 0.012 199.0 -70: (ns/day) (hour/ns) -70: Performance: 62.350 0.385 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (53 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: NVE simulation: will use the initial temperature of 456.887 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 6 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 198.8 -70: (ns/day) (hour/ns) -70: Performance: 189.045 0.127 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 198.9 -70: (ns/day) (hour/ns) -70: Performance: 100.732 0.238 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.3 -70: (ns/day) (hour/ns) -70: Performance: 98.007 0.245 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (48 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.0 -70: (ns/day) (hour/ns) -70: Performance: 170.460 0.141 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 199.0 -70: (ns/day) (hour/ns) -70: Performance: 101.648 0.236 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.7 -70: (ns/day) (hour/ns) -70: Performance: 94.053 0.255 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (68 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.1 -70: (ns/day) (hour/ns) -70: Performance: 146.754 0.164 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.008 198.9 -70: (ns/day) (hour/ns) -70: Performance: 102.870 0.233 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.0 -70: (ns/day) (hour/ns) -70: Performance: 96.388 0.249 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (135 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.2 -70: (ns/day) (hour/ns) -70: Performance: 147.017 0.163 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.1 -70: (ns/day) (hour/ns) -70: Performance: 78.927 0.304 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.023 0.012 198.9 -70: (ns/day) (hour/ns) -70: Performance: 66.916 0.359 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (73 ms) -70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: -70: NOTE 3 [file unknown]: -70: You are using constraints on all bonds, whereas the forcefield has been -70: parametrized only with constraints involving hydrogen atoms. We suggest -70: using constraints = h-bonds instead, this will also improve performance. -70: -70: Number of degrees of freedom in T-Coupling group System is 23.00 -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: There are 9 non-linear virtual site constructions. Their contribution to -70: the energy error is approximated. In most cases this does not affect the -70: error significantly. -70: -70: -70: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 5 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -70: -70: turning all bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -70: -70: Cleaning up constraints and constant bonded interactions with virtual sites -70: -70: Removed 18 Angles with virtual sites, 21 left -70: -70: Removed 10 Proper Dih.s with virtual sites, 44 left -70: -70: Converted 15 Constraints with virtual sites to connections, 7 left -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.010 199.2 -70: (ns/day) (hour/ns) -70: Performance: 140.878 0.170 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.1 -70: (ns/day) (hour/ns) -70: Performance: 95.112 0.252 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 -70: -70: Update groups can not be used for this system because an incompatible virtual site type is used -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine dipeptide in vacuo' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 198.8 -70: (ns/day) (hour/ns) -70: Performance: 80.368 0.299 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (87 ms) -70: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1641 ms total) -70: -70: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.0 -70: (ns/day) (hour/ns) -70: Performance: 134.976 0.178 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 198.4 -70: (ns/day) (hour/ns) -70: Performance: 81.391 0.295 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.025 0.013 199.1 -70: (ns/day) (hour/ns) -70: Performance: 61.916 0.388 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (56 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.0 -70: (ns/day) (hour/ns) -70: Performance: 135.627 0.177 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.026 0.013 198.4 -70: (ns/day) (hour/ns) -70: Performance: 60.297 0.398 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.024 0.012 199.1 -70: (ns/day) (hour/ns) -70: Performance: 64.841 0.370 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (63 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.033 0.017 199.7 -70: (ns/day) (hour/ns) -70: Performance: 88.800 0.270 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.062 0.031 199.8 -70: (ns/day) (hour/ns) -70: Performance: 24.879 0.965 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.036 0.018 199.5 -70: (ns/day) (hour/ns) -70: Performance: 43.654 0.550 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (91 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: NVE simulation: will use the initial temperature of 294.908 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 4 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.036 0.018 199.6 -70: (ns/day) (hour/ns) -70: Performance: 80.390 0.299 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.025 0.013 199.6 -70: (ns/day) (hour/ns) -70: Performance: 61.605 0.390 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.049 0.025 199.4 -70: (ns/day) (hour/ns) -70: Performance: 31.490 0.762 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (84 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 198.5 -70: (ns/day) (hour/ns) -70: Performance: 139.326 0.172 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 198.3 -70: (ns/day) (hour/ns) -70: Performance: 88.244 0.272 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 198.8 -70: (ns/day) (hour/ns) -70: Performance: 96.051 0.250 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (68 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 198.8 -70: (ns/day) (hour/ns) -70: Performance: 152.804 0.157 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.3 -70: (ns/day) (hour/ns) -70: Performance: 87.439 0.274 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.8 -70: (ns/day) (hour/ns) -70: Performance: 87.802 0.273 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (147 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.9 -70: (ns/day) (hour/ns) -70: Performance: 159.041 0.151 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 198.3 -70: (ns/day) (hour/ns) -70: Performance: 88.983 0.270 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.9 -70: (ns/day) (hour/ns) -70: Performance: 84.291 0.285 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (61 ms) -70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.023 0.011 199.0 -70: (ns/day) (hour/ns) -70: Performance: 128.156 0.187 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.3 -70: (ns/day) (hour/ns) -70: Performance: 86.445 0.278 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 198.8 -70: (ns/day) (hour/ns) -70: Performance: 88.881 0.270 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (69 ms) -70: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (643 ms total) -70: -70: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 198.4 -70: (ns/day) (hour/ns) -70: Performance: 222.091 0.108 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.006 198.8 -70: (ns/day) (hour/ns) -70: Performance: 137.372 0.175 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.8 -70: (ns/day) (hour/ns) -70: Performance: 134.240 0.179 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (29 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.8 -70: (ns/day) (hour/ns) -70: Performance: 251.854 0.095 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.005 198.8 -70: (ns/day) (hour/ns) -70: Performance: 141.656 0.169 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 199.2 -70: (ns/day) (hour/ns) -70: Performance: 81.198 0.296 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (31 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 199.0 -70: (ns/day) (hour/ns) -70: Performance: 220.367 0.109 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.9 -70: (ns/day) (hour/ns) -70: Performance: 130.241 0.184 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.006 199.0 -70: (ns/day) (hour/ns) -70: Performance: 120.894 0.199 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (29 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 199.1 -70: (ns/day) (hour/ns) -70: Performance: 210.604 0.114 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 198.8 -70: (ns/day) (hour/ns) -70: Performance: 112.940 0.213 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 199.0 -70: (ns/day) (hour/ns) -70: Performance: 117.168 0.205 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (31 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 164.629 0.146 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.5 -70: (ns/day) (hour/ns) -70: Performance: 87.522 0.274 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 199.0 -70: (ns/day) (hour/ns) -70: Performance: 107.495 0.223 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (35 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.2 -70: (ns/day) (hour/ns) -70: Performance: 161.407 0.149 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.4 -70: (ns/day) (hour/ns) -70: Performance: 95.937 0.250 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.0 -70: (ns/day) (hour/ns) -70: Performance: 95.234 0.252 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (36 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 171.542 0.140 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.5 -70: (ns/day) (hour/ns) -70: Performance: 95.240 0.252 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.1 -70: (ns/day) (hour/ns) -70: Performance: 87.573 0.274 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (38 ms) -70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.4 -70: (ns/day) (hour/ns) -70: Performance: 173.685 0.138 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.4 -70: (ns/day) (hour/ns) -70: Performance: 95.510 0.251 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 -70: -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 198.7 -70: (ns/day) (hour/ns) -70: Performance: 105.838 0.227 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (35 ms) -70: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (267 ms total) -70: -70: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact -70: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 198.9 -70: (ns/day) (hour/ns) -70: Performance: 214.014 0.112 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 199.3 -70: (ns/day) (hour/ns) -70: Performance: 73.152 0.328 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.006 198.9 -70: (ns/day) (hour/ns) -70: Performance: 121.743 0.197 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (35 ms) -70: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 68.810 K for -70: determining the Verlet buffer size -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.2 -70: (ns/day) (hour/ns) -70: Performance: 180.045 0.133 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.5 -70: (ns/day) (hour/ns) -70: Performance: 85.364 0.281 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.1 -70: (ns/day) (hour/ns) -70: Performance: 91.558 0.262 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (36 ms) -70: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (71 ms total) -70: -70: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 198.8 -70: (ns/day) (hour/ns) -70: Performance: 202.113 0.119 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.5 -70: (ns/day) (hour/ns) -70: Performance: 129.816 0.185 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.8 -70: (ns/day) (hour/ns) -70: Performance: 126.650 0.189 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (30 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.014 0.007 198.3 -70: (ns/day) (hour/ns) -70: Performance: 208.030 0.115 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 199.0 -70: (ns/day) (hour/ns) -70: Performance: 105.752 0.227 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.012 0.006 198.9 -70: (ns/day) (hour/ns) -70: Performance: 127.877 0.188 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (31 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 198.6 -70: (ns/day) (hour/ns) -70: Performance: 216.564 0.111 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.005 198.2 -70: (ns/day) (hour/ns) -70: Performance: 141.533 0.170 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.2 -70: (ns/day) (hour/ns) -70: Performance: 87.029 0.276 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (31 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: -70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -70: 1 -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.013 0.007 199.0 -70: (ns/day) (hour/ns) -70: Performance: 219.426 0.109 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.011 0.006 198.8 -70: (ns/day) (hour/ns) -70: Performance: 135.450 0.177 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.015 0.007 199.1 -70: (ns/day) (hour/ns) -70: Performance: 104.091 0.231 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (30 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.3 -70: (ns/day) (hour/ns) -70: Performance: 161.382 0.149 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.5 -70: (ns/day) (hour/ns) -70: Performance: 91.261 0.263 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.1 -70: (ns/day) (hour/ns) -70: Performance: 99.740 0.241 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (35 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 179.269 0.134 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 199.6 -70: (ns/day) (hour/ns) -70: Performance: 87.432 0.274 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.1 -70: (ns/day) (hour/ns) -70: Performance: 94.468 0.254 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (35 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 -70: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) -70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 186.481 0.129 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.008 199.5 -70: (ns/day) (hour/ns) -70: Performance: 93.589 0.256 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.020 0.010 199.2 -70: (ns/day) (hour/ns) -70: Performance: 75.979 0.316 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (37 ms) -70: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (233 ms total) -70: -70: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact -70: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: MTTK coupling is deprecated and will soon be removed -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: MTTK coupling is deprecated and will soon be removed -70: -70: Number of degrees of freedom in T-Coupling group System is 33.00 -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps. -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 1 of the 1 non-bonded parameter combinations -70: -70: Excluding 1 bonded neighbours molecule type 'Argon' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.010 199.1 -70: (ns/day) (hour/ns) -70: Performance: 140.528 0.171 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.016 0.008 199.3 -70: (ns/day) (hour/ns) -70: Performance: 97.781 0.245 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Argon' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.017 0.009 199.1 -70: (ns/day) (hour/ns) -70: Performance: 90.121 0.266 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (38 ms) -70: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (38 ms total) -70: -70: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact -70: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.023 0.012 199.1 -70: (ns/day) (hour/ns) -70: Performance: 126.868 0.189 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.019 0.010 198.8 -70: (ns/day) (hour/ns) -70: Performance: 80.596 0.298 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.1 -70: (ns/day) (hour/ns) -70: Performance: 70.055 0.343 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (44 ms) -70: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There were 3 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'FirstWaterMolecule' has 3 atoms -70: Pull group 2 'SecondWaterMolecule' has 3 atoms -70: Number of degrees of freedom in T-Coupling group System is 9.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 2573.591 K for -70: determining the Verlet buffer size -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 3 2 -70: 2 3 5 1.112 nm 1.000 nm -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps. -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 3 of the 3 non-bonded parameter combinations -70: -70: Generated 3 of the 3 1-4 parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.021 0.011 199.2 -70: (ns/day) (hour/ns) -70: Performance: 138.627 0.173 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.026 0.013 199.6 -70: (ns/day) (hour/ns) -70: Performance: 59.451 0.404 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc2' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.018 0.009 198.7 -70: (ns/day) (hour/ns) -70: Performance: 83.796 0.286 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (45 ms) -70: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (89 ms total) -70: -70: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact -70: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: Setting the AWH bias MC random seed to -146806185 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'C_&_r_1' has 1 atoms -70: Pull group 2 'N_&_r_2' has 1 atoms -70: Pull group 3 'CA' has 1 atoms -70: Pull group 4 'C_&_r_2' has 1 atoms -70: Pull group 5 'N_&_r_3' has 1 atoms -70: Number of degrees of freedom in T-Coupling group System is 51.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 1 0 -70: 2 1 0 179.098 deg 0.000 deg -70: 2 1 0 -70: 3 1 0 158.667 deg 0.000 deg -70: -70: There were 3 NOTEs -70: Setting the AWH bias MC random seed to -79691905 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'C_&_r_1' has 1 atoms -70: Pull group 2 'N_&_r_2' has 1 atoms -70: Pull group 3 'CA' has 1 atoms -70: Pull group 4 'C_&_r_2' has 1 atoms -70: Pull group 5 'N_&_r_3' has 1 atoms -70: Number of degrees of freedom in T-Coupling group System is 51.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 1 0 -70: 2 1 0 179.098 deg 0.000 deg -70: 2 1 0 -70: 3 1 0 158.667 deg 0.000 deg -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.030 0.015 199.1 -70: (ns/day) (hour/ns) -70: Performance: 98.407 0.244 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.023 0.012 198.9 -70: (ns/day) (hour/ns) -70: Performance: 67.236 0.357 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.059 0.029 199.5 -70: (ns/day) (hour/ns) -70: Performance: 26.401 0.909 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (87 ms) -70: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 -70: Setting the AWH bias MC random seed to -68436003 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'C_&_r_1' has 1 atoms -70: Pull group 2 'N_&_r_2' has 1 atoms -70: Pull group 3 'CA' has 1 atoms -70: Pull group 4 'C_&_r_2' has 1 atoms -70: Pull group 5 'N_&_r_3' has 1 atoms -70: Number of degrees of freedom in T-Coupling group System is 51.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 1 0 -70: 2 1 0 179.098 deg 0.000 deg -70: 2 1 0 -70: 3 1 0 158.667 deg 0.000 deg -70: -70: There were 3 NOTEs -70: Setting the AWH bias MC random seed to -134226244 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: Setting nstcalcenergy (100) equal to nstenergy (4) -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Pull group 1 'C_&_r_1' has 1 atoms -70: Pull group 2 'N_&_r_2' has 1 atoms -70: Pull group 3 'CA' has 1 atoms -70: Pull group 4 'C_&_r_2' has 1 atoms -70: Pull group 5 'N_&_r_3' has 1 atoms -70: Number of degrees of freedom in T-Coupling group System is 51.00 -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: Pull group natoms pbc atom distance at start reference at t=0 -70: 1 1 0 -70: 2 1 0 179.098 deg 0.000 deg -70: 2 1 0 -70: 3 1 0 158.667 deg 0.000 deg -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 16 steps, 0.0 ps. -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2145 of the 2145 non-bonded parameter combinations -70: -70: Generated 2145 of the 2145 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.089 0.044 199.7 -70: (ns/day) (hour/ns) -70: Performance: 33.075 0.726 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.051 0.026 199.5 -70: (ns/day) (hour/ns) -70: Performance: 30.208 0.794 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'Alanine-dipeptide' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.024 0.012 198.4 -70: (ns/day) (hour/ns) -70: Performance: 63.389 0.379 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (113 ms) -70: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (201 ms total) -70: -70: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact -70: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -70: that with the Verlet scheme, nstlist has no effect on the accuracy of -70: your simulation. -70: -70: Generating 1-4 interactions: fudge = 0.5 -70: Number of degrees of freedom in T-Coupling group System is 79.00 -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps. -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: Generated 2485 of the 2485 non-bonded parameter combinations -70: -70: Generated 2485 of the 2485 1-4 parameter combinations -70: -70: Excluding 3 bonded neighbours molecule type 'nonanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -70: -70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -70: -70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.028 0.014 199.6 -70: (ns/day) (hour/ns) -70: Performance: 103.593 0.232 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 8 steps, 0.0 ps. -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 199.5 -70: (ns/day) (hour/ns) -70: Performance: 69.076 0.347 -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun '30 atom system in water' -70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.022 0.011 198.9 -70: (ns/day) (hour/ns) -70: Performance: 70.221 0.342 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (71 ms) -70: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (71 ms total) -70: -70: [----------] 3 tests from Checking/InitialConstraintsTest -70: [ RUN ] Checking/InitialConstraintsTest.Works/0 -70: Number of degrees of freedom in T-Coupling group rest is 11.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -70: NVE simulation: will use the initial temperature of 1141.954 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc-and-methanol' -70: 1 steps, 0.0 ps. -70: Setting the LD random seed to 1575583615 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.030 0.015 199.5 -70: (ns/day) (hour/ns) -70: Performance: 11.510 2.085 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (19 ms) -70: [ RUN ] Checking/InitialConstraintsTest.Works/1 -70: Number of degrees of freedom in T-Coupling group rest is 11.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -70: NVE simulation: will use the initial temperature of 1141.954 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 2 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc-and-methanol' -70: 1 steps, 0.0 ps. -70: Setting the LD random seed to -562118669 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.034 0.017 199.6 -70: (ns/day) (hour/ns) -70: Performance: 10.058 2.386 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (21 ms) -70: [ RUN ] Checking/InitialConstraintsTest.Works/2 -70: -70: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -70: Integrator method md-vv-avek is implemented primarily for validation -70: purposes; for molecular dynamics, you should probably be using md or -70: md-vv -70: -70: Number of degrees of freedom in T-Coupling group rest is 11.00 -70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -70: -70: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -70: NVE simulation: will use the initial temperature of 1141.954 K for -70: determining the Verlet buffer size -70: -70: -70: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: -70: You are using a plain Coulomb cut-off, which might produce artifacts. -70: You might want to consider using PME electrostatics. -70: -70: -70: -70: There were 3 NOTEs -70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -70: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -70: Can not increase nstlist because an NVE ensemble is used -70: Using 1 MPI process -70: Using 2 OpenMP threads -70: -70: -70: NOTE: The number of threads is not equal to the number of (logical) cpus -70: and the -pin option is set to auto: will not pin threads to cpus. -70: This can lead to significant performance degradation. -70: Consider using -pin on (and -pinoffset in case you run multiple jobs). -70: starting mdrun 'spc-and-methanol' -70: 1 steps, 0.0 ps. -70: Setting the LD random seed to -605377575 -70: -70: Generated 8 of the 10 non-bonded parameter combinations -70: -70: Excluding 2 bonded neighbours molecule type 'Methanol' -70: -70: turning H bonds into constraints... -70: -70: Excluding 2 bonded neighbours molecule type 'SOL' -70: -70: turning H bonds into constraints... -70: -70: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -70: -70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K -70: -70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm -70: -70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm -70: -70: Note that mdrun will redetermine rlist based on the actual pair-list setup -70: -70: This run will generate roughly 0 Mb of data -70: -70: Writing final coordinates. -70: -70: Core t (s) Wall t (s) (%) -70: Time: 0.008 0.004 197.7 -70: (ns/day) (hour/ns) -70: Performance: 42.011 0.571 -70: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file -70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (8 ms) -70: [----------] 3 tests from Checking/InitialConstraintsTest (50 ms total) -70: -70: [----------] Global test environment tear-down -70: [==========] 76 tests from 13 test suites ran. (3789 ms total) -70: [ PASSED ] 76 tests. -70/96 Test #70: MdrunIOTests ................................. Passed 3.99 sec -test 71 - Start 71: MdrunTestsOneRank - -71: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" -71: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -71: Test timeout computed to be: 600 -71: [==========] Running 29 tests from 8 test suites. -71: [----------] Global test environment set-up. -71: [----------] 1 test from CompelTest -71: [ RUN ] CompelTest.SwapCanRun -71: Setting the LD random seed to 2127100667 -71: -71: Generated 330891 of the 330891 non-bonded parameter combinations -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 330891 of the 330891 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein' -71: -71: turning all bonds into constraints... -71: -71: Excluding 3 bonded neighbours molecule type 'OCT' -71: -71: turning all bonds into constraints... -71: -71: Excluding 1 bonded neighbours molecule type 'NA' -71: -71: turning all bonds into constraints... -71: -71: Excluding 1 bonded neighbours molecule type 'CL' -71: -71: turning all bonds into constraints... -71: -71: Excluding 3 bonded neighbours molecule type 'Protein' -71: -71: Excluding 3 bonded neighbours molecule type 'OCT' -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: turning all bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -71: Split0 group 'Ch0' contains 83 atoms. -71: Split1 group 'Ch1' contains 83 atoms. -71: Solvent group 'SOL' contains 11931 atoms. -71: Swap group 'NA+' contains 19 atoms. -71: Swap group 'CL-' contains 19 atoms. -71: Number of degrees of freedom in T-Coupling group System is 27869.00 -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -71: -71: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -71: Removing center of mass motion in the presence of position restraints -71: might cause artifacts. When you are using position restraints to -71: equilibrate a macro-molecule, the artifacts are usually negligible. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 2 NOTEs -71: -71: This run will generate roughly 1 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Update groups can not be used for this system because there are three or more consecutively coupled constraints -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: SWAP: Determining initial numbers of ions per compartment. -71: SWAP: Setting pointers for checkpoint writing -71: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -71: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -71: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -71: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -71: starting mdrun 'Channel_coco in octane membrane' -71: 2 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: NOTE: 37 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.192 0.096 199.8 -71: (ns/day) (hour/ns) -71: Performance: 13.509 1.777 -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -71: -71: Update groups can not be used for this system because there are three or more consecutively coupled constraints -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: SWAP: Setting pointers for checkpoint writing -71: SWAP: Copying channel fluxes from checkpoint file data -71: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -71: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -71: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -71: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -71: starting mdrun 'Channel_coco in octane membrane' -71: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -71: -71: Writing final coordinates. -71: -71: NOTE: 23 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.135 0.068 199.8 -71: (ns/day) (hour/ns) -71: Performance: 19.191 1.251 -71: [ OK ] CompelTest.SwapCanRun (479 ms) -71: [----------] 1 test from CompelTest (479 ms total) -71: -71: [----------] 6 tests from BondedInteractionsTest -71: [ RUN ] BondedInteractionsTest.NormalBondWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to 2142895918 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 2 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 19 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.001 0.000 187.3 -71: (ns/day) (hour/ns) -71: Performance: 231.558 0.104 -71: [ OK ] BondedInteractionsTest.NormalBondWorks (5 ms) -71: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to -775946499 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 2 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 16 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.000 0.000 184.5 -71: (ns/day) (hour/ns) -71: Performance: 346.783 0.069 -71: [ OK ] BondedInteractionsTest.TabulatedBondWorks (5 ms) -71: [ RUN ] BondedInteractionsTest.NormalAngleWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to -822781633 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 4 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 11 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.001 0.000 187.8 -71: (ns/day) (hour/ns) -71: Performance: 209.958 0.114 -71: [ OK ] BondedInteractionsTest.NormalAngleWorks (5 ms) -71: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to -1345333641 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 4 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 17 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.000 0.000 183.5 -71: (ns/day) (hour/ns) -71: Performance: 351.833 0.068 -71: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (5 ms) -71: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to 871183359 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 4 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 17 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.000 0.000 185.5 -71: (ns/day) (hour/ns) -71: Performance: 331.857 0.072 -71: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) -71: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to 1610610427 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'butane' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -71: In moleculetype 'butane' 4 atoms are not bound by a potential or -71: constraint to any other atom in the same moleculetype. Although -71: technically this might not cause issues in a simulation, this often means -71: that the user forgot to add a bond/potential/constraint or put multiple -71: molecules in the same moleculetype definition by mistake. Run with -v to -71: get information for each atom. -71: -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -71: NVE simulation with an initial temperature of zero: will use a Verlet -71: buffer of 10%. Check your energy drift! -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -71: -71: Reading frames from gro file 'A single butane', 4 atoms. -71: Reading frame 0 time 0.000 Last frame 0 time 0.000 -71: -71: NOTE: 19 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.000 0.000 184.8 -71: (ns/day) (hour/ns) -71: Performance: 357.384 0.067 -71: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (5 ms) -71: [----------] 6 tests from BondedInteractionsTest (30 ms total) -71: -71: [----------] 2 tests from BoxDeformationTest -71: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (10) -71: -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -71: For a correct single-point energy evaluation with nsteps = 0, use -71: continuation = yes to avoid constraining the input coordinates. -71: -71: Setting the LD random seed to -1094230785 -71: -71: Generated 1 of the 1 non-bonded parameter combinations -71: -71: Excluding 1 bonded neighbours molecule type 'Argon' -71: -71: Setting gen_seed to -25334849 -71: -71: Velocities were taken from a Maxwell distribution at 0 K -71: -71: This run will generate roughly 0 Mb of data -71: Number of degrees of freedom in T-Coupling group rest is 33.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Argon' -71: 0 steps, 0.0 ps. -71: -71: NOTE: 25 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.000 0.000 160.6 -71: (ns/day) (hour/ns) -71: Performance: 699.590 0.034 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (5 ms) -71: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (10) -71: -71: Setting the LD random seed to -1628644353 -71: -71: Generated 330891 of the 330891 non-bonded parameter combinations -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 330891 of the 330891 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -71: Number of degrees of freedom in T-Coupling group rest is 1293.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -71: -71: Estimate for the relative computational load of the PME mesh part: 0.20 -71: -71: This run will generate roughly 0 Mb of data -71: -71: There were 2 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 20 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.300 0.150 199.9 -71: (ns/day) (hour/ns) -71: Performance: 24.219 0.991 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (377 ms) -71: [----------] 2 tests from BoxDeformationTest (383 ms total) -71: -71: [----------] 1 test from PositionRestraintCommTest -71: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -71: You have set rlist larger than the interaction cut-off, but you also have -71: verlet-buffer-tolerance > 0. Will set rlist using -71: verlet-buffer-tolerance. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (10) -71: -71: Setting the LD random seed to 402571259 -71: -71: Generated 330891 of the 330891 non-bonded parameter combinations -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 330891 of the 330891 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein' -71: -71: Excluding 3 bonded neighbours molecule type 'OCT' -71: -71: Excluding 1 bonded neighbours molecule type 'NA' -71: -71: Excluding 1 bonded neighbours molecule type 'CL' -71: -71: Excluding 3 bonded neighbours molecule type 'Protein' -71: -71: Excluding 3 bonded neighbours molecule type 'OCT' -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -71: 13489 atoms are not part of any of the VCM groups -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -71: 13489 atoms are not part of any center of mass motion removal group. -71: This may lead to artifacts. -71: In most cases one should use one group for the whole system. -71: -71: Number of degrees of freedom in T-Coupling group System is 29527.73 -71: -71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -71: Removing center of mass motion in the presence of position restraints -71: might cause artifacts. When you are using position restraints to -71: equilibrate a macro-molecule, the artifacts are usually negligible. -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: -71: Chain0: 2.207 2.168 7.330 -71: Chain1: 2.228 2.186 2.401 -71: Chain0: 2.207 2.168 7.330 -71: Chain1: 2.228 2.186 2.401 -71: -71: This run will generate roughly 1 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Channel_coco in octane membrane' -71: 10 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: NOTE: 15 % of the run time was spent in pair search, -71: you might want to increase nstlist (this has no effect on accuracy) -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.246 0.123 199.9 -71: (ns/day) (hour/ns) -71: Performance: 15.444 1.554 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (412 ms) -71: [----------] 1 test from PositionRestraintCommTest (412 ms total) -71: -71: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to -554254913 -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 2211 of the 2211 non-bonded parameter combinations -71: -71: Generated 2211 of the 2211 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -71: -71: NOTE 2 [file ala.top, line 256]: -71: For energy conservation with LINCS, lincs_iter should be 2 or larger. -71: -71: -71: Number of degrees of freedom in T-Coupling group rest is 54.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -71: -71: Estimate for the relative computational load of the PME mesh part: 0.94 -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 3 NOTEs -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'UNNAMED in water' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.015 0.008 198.6 -71: (ns/day) (hour/ns) -71: Performance: 56.042 0.428 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to 1073736669 -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 2211 of the 2211 non-bonded parameter combinations -71: -71: Generated 2211 of the 2211 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: NOTE 2 [file ala.top, line 256]: -71: For energy conservation with LINCS, lincs_iter should be 2 or larger. -71: -71: -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -71: Number of degrees of freedom in T-Coupling group rest is 54.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -71: -71: Estimate for the relative computational load of the PME mesh part: 0.94 -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'UNNAMED in water' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.015 0.007 198.7 -71: (ns/day) (hour/ns) -71: Performance: 58.610 0.409 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) -71: -71: -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (352 ms) -71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to 1063575167 -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 2211 of the 2211 non-bonded parameter combinations -71: -71: Generated 2211 of the 2211 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: NOTE 2 [file ala.top, line 256]: -71: For energy conservation with LINCS, lincs_iter should be 2 or larger. -71: -71: -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -71: Number of degrees of freedom in T-Coupling group rest is 54.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: There were 3 NOTEs -71: -71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -71: -71: Estimate for the relative computational load of the PME mesh part: 0.94 -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'UNNAMED in water' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.019 0.010 199.0 -71: (ns/day) (hour/ns) -71: Performance: 45.403 0.529 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to 2013003630 -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 2211 of the 2211 non-bonded parameter combinations -71: -71: Generated 2211 of the 2211 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -71: -71: turning H bonds into constraints... -71: -71: NOTE 2 [file ala.top, line 256]: -71: For energy conservation with LINCS, lincs_iter should be 2 or larger. -71: -71: -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -71: Number of degrees of freedom in T-Coupling group rest is 54.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -71: The optimal PME mesh load for parallel simulations is below 0.5 -71: and for highly parallel simulations between 0.25 and 0.33, -71: for higher performance, increase the cut-off and the PME grid spacing. -71: -71: -71: -71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -71: Calculating fourier grid dimensions for X Y Z -71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -71: -71: There were 3 NOTEs -71: -71: Estimate for the relative computational load of the PME mesh part: 0.94 -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -71: Can not increase nstlist because an NVE ensemble is used -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'UNNAMED in water' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.012 0.006 198.4 -71: (ns/day) (hour/ns) -71: Performance: 71.553 0.335 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -71: -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (40 ms) -71: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (393 ms total) -71: -71: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to -615045 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -71: Generating 1-4 interactions: fudge = 0.5 -71: Pull group 1 'FirstWaterMolecule' has 3 atoms -71: Pull group 2 'SecondWaterMolecule' has 3 atoms -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: Pull group natoms pbc atom distance at start reference at t=0 -71: 1 3 2 -71: 2 3 5 1.112 nm 1.000 nm -71: -71: There was 1 NOTE -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.024 0.012 198.6 -71: (ns/day) (hour/ns) -71: Performance: 35.786 0.671 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: Setting the LD random seed to -317057 -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -71: Pull group 1 'FirstWaterMolecule' has 3 atoms -71: Pull group 2 'SecondWaterMolecule' has 3 atoms -71: Number of degrees of freedom in T-Coupling group rest is 9.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: Pull group natoms pbc atom distance at start reference at t=0 -71: 1 3 2 -71: 2 3 5 1.112 nm 1.000 nm -71: -71: There was 1 NOTE -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -71: Can not increase nstlist because an NVE ensemble is used -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 4 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.028 0.014 198.7 -71: (ns/day) (hour/ns) -71: Performance: 31.154 0.770 -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -71: -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -71: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (37 ms) -71: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (37 ms total) -71: -71: [----------] 12 tests from FreezeWorks/FreezeGroupTest -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: NVE simulation: will use the initial temperature of 246.451 K for -71: determining the Verlet buffer size -71: -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -71: -71: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 5 NOTEs -71: -71: There was 1 WARNING -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.017 0.008 198.5 -71: (ns/day) (hour/ns) -71: Performance: 93.367 0.257 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (18 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: NVE simulation: will use the initial temperature of 246.451 K for -71: determining the Verlet buffer size -71: -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 5 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.019 0.010 198.8 -71: (ns/day) (hour/ns) -71: Performance: 81.535 0.294 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (20 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: NVE simulation: will use the initial temperature of 246.451 K for -71: determining the Verlet buffer size -71: -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 5 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.020 0.010 198.6 -71: (ns/day) (hour/ns) -71: Performance: 77.845 0.308 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (21 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: NVE simulation: will use the initial temperature of 246.451 K for -71: determining the Verlet buffer size -71: -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 5 NOTEs -71: -71: There was 1 WARNING -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.021 0.010 198.8 -71: (ns/day) (hour/ns) -71: Performance: 74.409 0.323 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (22 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: NVE simulation: will use the initial temperature of 246.451 K for -71: determining the Verlet buffer size -71: -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 5 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.017 0.009 198.9 -71: (ns/day) (hour/ns) -71: Performance: 88.587 0.271 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (19 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -71: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped -71: Parrinello-Rahman is not implemented in md-vv. -71: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.013 0.007 198.9 -71: (ns/day) (hour/ns) -71: Performance: 116.883 0.205 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (18 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.017 0.008 198.9 -71: (ns/day) (hour/ns) -71: Performance: 91.695 0.262 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (20 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.012 0.006 198.5 -71: (ns/day) (hour/ns) -71: Performance: 124.579 0.193 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (18 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.014 0.007 198.9 -71: (ns/day) (hour/ns) -71: Performance: 112.835 0.213 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (34 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.011 0.005 198.3 -71: (ns/day) (hour/ns) -71: Performance: 143.982 0.167 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (34 ms) -71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 2145 of the 2145 non-bonded parameter combinations -71: -71: Generated 2145 of the 2145 1-4 parameter combinations -71: -71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -71: -71: turning H bonds into constraints... -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -71: There are 5 atoms that are fully frozen and part of COMM removal -71: group(s), removing these atoms from the COMM removal group(s) -71: -71: -71: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -71: There are 3 atoms that are frozen along less then 3 dimensions and part -71: of COMM removal group(s), due to limitations in the code these still -71: contribute to the mass of the COM along frozen dimensions and therefore -71: the COMM correction will be too small. -71: -71: Number of degrees of freedom in T-Coupling group System is 33.00 -71: -71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -71: -71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -71: -71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -71: -71: Note that mdrun will redetermine rlist based on the actual pair-list setup -71: -71: This run will generate roughly 0 Mb of data -71: -71: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -71: You are using a plain Coulomb cut-off, which might produce artifacts. -71: You might want to consider using PME electrostatics. -71: -71: -71: -71: There were 4 NOTEs -71: -71: There was 1 WARNING -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -71: -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'Alanine-dipeptide' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.012 0.006 198.5 -71: (ns/day) (hour/ns) -71: Performance: 124.489 0.193 -71: -71: -71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (33 ms) -71: [----------] 12 tests from FreezeWorks/FreezeGroupTest (263 ms total) -71: -71: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Setting gen_seed to 1199561452 -71: -71: Velocities were taken from a Maxwell distribution at 0 K -71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: Net Acceleration in X direction, will not be corrected -71: Net Acceleration in Y direction, will not be corrected -71: Net Acceleration in Z direction, will not be corrected -71: -71: There were 3 NOTEs -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.011 0.005 198.7 -71: (ns/day) (hour/ns) -71: Performance: 285.883 0.084 -71: -71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (10 ms) -71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Setting gen_seed to -1474561 -71: -71: Velocities were taken from a Maxwell distribution at 0 K -71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -71: Net Acceleration in X direction, will not be corrected -71: Net Acceleration in Y direction, will not be corrected -71: Net Acceleration in Z direction, will not be corrected -71: -71: There were 3 NOTEs -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because verlet-buffer-tolerance is not set or used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.044 0.022 199.6 -71: (ns/day) (hour/ns) -71: Performance: 71.323 0.336 -71: -71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (26 ms) -71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generating 1-4 interactions: fudge = 0.5 -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Setting gen_seed to 1840381247 -71: -71: Velocities were taken from a Maxwell distribution at 0 K -71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -71: Net Acceleration in X direction, will not be corrected -71: Net Acceleration in Y direction, will not be corrected -71: Net Acceleration in Z direction, will not be corrected -71: -71: There were 3 NOTEs -71: -71: This run will generate roughly 0 Mb of data -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because an NVE ensemble is used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.020 0.010 199.0 -71: (ns/day) (hour/ns) -71: Performance: 154.929 0.155 -71: -71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (15 ms) -71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -71: -71: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -71: that with the Verlet scheme, nstlist has no effect on the accuracy of -71: your simulation. -71: -71: -71: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -71: < 0 -71: -71: -71: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -71: Setting nstcalcenergy (100) equal to nstenergy (4) -71: -71: Generated 3 of the 3 non-bonded parameter combinations -71: -71: Generated 3 of the 3 1-4 parameter combinations -71: Generating 1-4 interactions: fudge = 0.5 -71: -71: Excluding 2 bonded neighbours molecule type 'SOL' -71: -71: Setting gen_seed to -201331205 -71: -71: Velocities were taken from a Maxwell distribution at 0 K -71: -71: This run will generate roughly 0 Mb of data -71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -71: Net Acceleration in X direction, will not be corrected -71: Net Acceleration in Y direction, will not be corrected -71: Net Acceleration in Z direction, will not be corrected -71: -71: There were 3 NOTEs -71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -71: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -71: Can not increase nstlist because verlet-buffer-tolerance is not set or used -71: Using 1 MPI process -71: Using 2 OpenMP threads -71: -71: -71: NOTE: The number of threads is not equal to the number of (logical) cpus -71: and the -pin option is set to auto: will not pin threads to cpus. -71: This can lead to significant performance degradation. -71: Consider using -pin on (and -pinoffset in case you run multiple jobs). -71: starting mdrun 'spc2' -71: 8 steps, 0.0 ps. -71: -71: Writing final coordinates. -71: -71: Core t (s) Wall t (s) (%) -71: Time: 0.013 0.007 198.4 -71: (ns/day) (hour/ns) -71: Performance: 233.681 0.103 -71: -71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (11 ms) -71: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (63 ms total) -71: -71: [----------] Global test environment tear-down -71: [==========] 29 tests from 8 test suites ran. (2248 ms total) -71: [ PASSED ] 28 tests. -71: [ SKIPPED ] 1 test, listed below: -71: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -71/96 Test #71: MdrunTestsOneRank ............................ Passed 2.52 sec -test 72 - Start 72: MdrunTestsTwoRanks - -72: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" -72: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -72: Test timeout computed to be: 600 -72: [==========] Running 29 tests from 8 test suites. -72: [----------] Global test environment set-up. -72: [----------] 1 test from CompelTest -72: [ RUN ] CompelTest.SwapCanRun -72: Setting the LD random seed to -956727323 -72: -72: Generated 330891 of the 330891 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein' -72: -72: turning all bonds into constraints... -72: -72: Excluding 3 bonded neighbours molecule type 'OCT' -72: -72: turning all bonds into constraints... -72: -72: Excluding 1 bonded neighbours molecule type 'NA' -72: -72: turning all bonds into constraints... -72: -72: Excluding 1 bonded neighbours molecule type 'CL' -72: -72: turning all bonds into constraints... -72: -72: Excluding 3 bonded neighbours molecule type 'Protein' -72: -72: Excluding 3 bonded neighbours molecule type 'OCT' -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: turning all bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -72: Split0 group 'Ch0' contains 83 atoms. -72: Split1 group 'Ch1' contains 83 atoms. -72: Solvent group 'SOL' contains 11931 atoms. -72: Swap group 'NA+' contains 19 atoms. -72: Swap group 'CL-' contains 19 atoms. -72: Number of degrees of freedom in T-Coupling group System is 27869.00 -72: -72: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -72: -72: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -72: Removing center of mass motion in the presence of position restraints -72: might cause artifacts. When you are using position restraints to -72: equilibrate a macro-molecule, the artifacts are usually negligible. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: This run will generate roughly 1 Mb of data -72: -72: There were 2 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Update groups can not be used for this system because there are three or more consecutively coupled constraints -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: SWAP: Determining initial numbers of ions per compartment. -72: SWAP: Setting pointers for checkpoint writing -72: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -72: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -72: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -72: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -72: starting mdrun 'Channel_coco in octane membrane' -72: 2 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 1.9%. -72: The balanceable part of the MD step is 18%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.3%. -72: -72: -72: NOTE: 6 % of the run time was spent in domain decomposition, -72: 27 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.301 0.075 399.5 -72: (ns/day) (hour/ns) -72: Performance: 17.223 1.393 -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps -72: -72: Update groups can not be used for this system because there are three or more consecutively coupled constraints -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: SWAP: Setting pointers for checkpoint writing -72: SWAP: Copying channel fluxes from checkpoint file data -72: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules -72: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules -72: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules -72: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules -72: starting mdrun 'Channel_coco in octane membrane' -72: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). -72: -72: Writing final coordinates. -72: -72: NOTE: 18 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.209 0.052 399.3 -72: (ns/day) (hour/ns) -72: Performance: 24.801 0.968 -72: [ OK ] CompelTest.SwapCanRun (467 ms) -72: [----------] 1 test from CompelTest (467 ms total) -72: -72: [----------] 6 tests from BondedInteractionsTest -72: [ RUN ] BondedInteractionsTest.NormalBondWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -67119107 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 2 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 20 % of the run time was spent in domain decomposition, -72: 19 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 378.7 -72: (ns/day) (hour/ns) -72: Performance: 237.087 0.101 -72: [ OK ] BondedInteractionsTest.NormalBondWorks (6 ms) -72: [ RUN ] BondedInteractionsTest.TabulatedBondWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -71350583 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 2 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 21 % of the run time was spent in domain decomposition, -72: 17 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 377.2 -72: (ns/day) (hour/ns) -72: Performance: 256.286 0.094 -72: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) -72: [ RUN ] BondedInteractionsTest.NormalAngleWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -168035669 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 4 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 20 % of the run time was spent in domain decomposition, -72: 14 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 367.0 -72: (ns/day) (hour/ns) -72: Performance: 232.598 0.103 -72: [ OK ] BondedInteractionsTest.NormalAngleWorks (6 ms) -72: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -254823954 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 4 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 21 % of the run time was spent in domain decomposition, -72: 17 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 376.7 -72: (ns/day) (hour/ns) -72: Performance: 263.939 0.091 -72: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (6 ms) -72: [ RUN ] BondedInteractionsTest.NormalDihedralWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -34769089 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 4 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 20 % of the run time was spent in domain decomposition, -72: 16 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 377.7 -72: (ns/day) (hour/ns) -72: Performance: 242.319 0.099 -72: [ OK ] BondedInteractionsTest.NormalDihedralWorks (6 ms) -72: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to -171247762 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'butane' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero -72: -72: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: -72: In moleculetype 'butane' 4 atoms are not bound by a potential or -72: constraint to any other atom in the same moleculetype. Although -72: technically this might not cause issues in a simulation, this often means -72: that the user forgot to add a bond/potential/constraint or put multiple -72: molecules in the same moleculetype definition by mistake. Run with -v to -72: get information for each atom. -72: -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: -72: NVE simulation with an initial temperature of zero: will use a Verlet -72: buffer of 10%. Check your energy drift! -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/butane1.gro' -72: -72: Reading frames from gro file 'A single butane', 4 atoms. -72: Reading frame 0 time 0.000 Last frame 0 time 0.000 -72: -72: NOTE: 21 % of the run time was spent in domain decomposition, -72: 17 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 376.7 -72: (ns/day) (hour/ns) -72: Performance: 258.941 0.093 -72: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (6 ms) -72: [----------] 6 tests from BondedInteractionsTest (39 ms total) -72: -72: [----------] 2 tests from BoxDeformationTest -72: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (10) -72: -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: -72: For a correct single-point energy evaluation with nsteps = 0, use -72: continuation = yes to avoid constraining the input coordinates. -72: -72: Setting the LD random seed to 1046838719 -72: -72: Generated 1 of the 1 non-bonded parameter combinations -72: -72: Excluding 1 bonded neighbours molecule type 'Argon' -72: -72: Setting gen_seed to -575823910 -72: -72: Velocities were taken from a Maxwell distribution at 0 K -72: Number of degrees of freedom in T-Coupling group rest is 33.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: There were 3 NOTEs -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Argon' -72: 0 steps, 0.0 ps. -72: -72: NOTE: 27 % of the run time was spent in domain decomposition, -72: 20 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.001 0.000 292.2 -72: (ns/day) (hour/ns) -72: Performance: 628.327 0.038 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (6 ms) -72: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (10) -72: -72: Setting the LD random seed to 2147351547 -72: -72: Generated 330891 of the 330891 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -72: Number of degrees of freedom in T-Coupling group rest is 1293.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 -72: Calculating fourier grid dimensions for X Y Z -72: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 -72: -72: Estimate for the relative computational load of the PME mesh part: 0.20 -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 2 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 20 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.9%. -72: The balanceable part of the MD step is 52%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.5%. -72: -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.059 0.015 398.1 -72: (ns/day) (hour/ns) -72: Performance: 243.462 0.099 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (266 ms) -72: [----------] 2 tests from BoxDeformationTest (272 ms total) -72: -72: [----------] 1 test from PositionRestraintCommTest -72: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -72: You have set rlist larger than the interaction cut-off, but you also have -72: verlet-buffer-tolerance > 0. Will set rlist using -72: verlet-buffer-tolerance. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (10) -72: -72: Setting the LD random seed to -504365095 -72: -72: Generated 330891 of the 330891 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 330891 of the 330891 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein' -72: -72: Excluding 3 bonded neighbours molecule type 'OCT' -72: -72: Excluding 1 bonded neighbours molecule type 'NA' -72: -72: Excluding 1 bonded neighbours molecule type 'CL' -72: -72: Excluding 3 bonded neighbours molecule type 'Protein' -72: -72: Excluding 3 bonded neighbours molecule type 'OCT' -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/OctaneSandwich.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -72: 13489 atoms are not part of any of the VCM groups -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -72: 13489 atoms are not part of any center of mass motion removal group. -72: This may lead to artifacts. -72: In most cases one should use one group for the whole system. -72: -72: Number of degrees of freedom in T-Coupling group System is 29527.73 -72: -72: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: Chain0: 2.207 2.168 7.330 -72: Chain1: 2.228 2.186 2.401 -72: Chain0: 2.207 2.168 7.330 -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: -72: Removing center of mass motion in the presence of position restraints -72: might cause artifacts. When you are using position restraints to -72: equilibrate a macro-molecule, the artifacts are usually negligible. -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: Chain1: 2.228 2.186 2.401 -72: -72: This run will generate roughly 1 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Channel_coco in octane membrane' -72: 10 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 11 % of the run time was spent in pair search, -72: you might want to increase nstlist (this has no effect on accuracy) -72: -72: NOTE: 21 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.268 0.067 399.3 -72: (ns/day) (hour/ns) -72: Performance: 28.329 0.847 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (364 ms) -72: [----------] 1 test from PositionRestraintCommTest (364 ms total) -72: -72: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest -72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to -160589825 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2211 of the 2211 non-bonded parameter combinations -72: -72: Generated 2211 of the 2211 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -72: -72: turning H bonds into constraints... -72: -72: NOTE 2 [file ala.top, line 256]: -72: For energy conservation with LINCS, lincs_iter should be 2 or larger. -72: -72: -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -72: Number of degrees of freedom in T-Coupling group rest is 54.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -72: Calculating fourier grid dimensions for X Y Z -72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -72: -72: Estimate for the relative computational load of the PME mesh part: 0.94 -72: -72: This run will generate roughly 0 Mb of data -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: The optimal PME mesh load for parallel simulations is below 0.5 -72: and for highly parallel simulations between 0.25 and 0.33, -72: for higher performance, increase the cut-off and the PME grid spacing. -72: -72: -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'UNNAMED in water' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 41 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.029 0.007 394.8 -72: (ns/day) (hour/ns) -72: Performance: 58.446 0.411 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to 1969143614 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2211 of the 2211 non-bonded parameter combinations -72: -72: Generated 2211 of the 2211 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -72: -72: turning H bonds into constraints... -72: -72: NOTE 2 [file ala.top, line 256]: -72: For energy conservation with LINCS, lincs_iter should be 2 or larger. -72: -72: -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -72: Number of degrees of freedom in T-Coupling group rest is 54.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -72: Calculating fourier grid dimensions for X Y Z -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: The optimal PME mesh load for parallel simulations is below 0.5 -72: and for highly parallel simulations between 0.25 and 0.33, -72: for higher performance, increase the cut-off and the PME grid spacing. -72: -72: -72: -72: There were 3 NOTEs -72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -72: -72: Estimate for the relative computational load of the PME mesh part: 0.94 -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'UNNAMED in water' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 43 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.026 0.007 394.6 -72: (ns/day) (hour/ns) -72: Performance: 65.240 0.368 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) -72: trr version: GMX_trn_file (single precision) -72: -72: -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: -72: -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (367 ms) -72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to -270532613 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2211 of the 2211 non-bonded parameter combinations -72: -72: Generated 2211 of the 2211 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -72: -72: turning H bonds into constraints... -72: -72: NOTE 2 [file ala.top, line 256]: -72: For energy conservation with LINCS, lincs_iter should be 2 or larger. -72: -72: -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -72: Number of degrees of freedom in T-Coupling group rest is 54.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -72: Calculating fourier grid dimensions for X Y Z -72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -72: -72: Estimate for the relative computational load of the PME mesh part: 0.94 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -72: The optimal PME mesh load for parallel simulations is below 0.5 -72: and for highly parallel simulations between 0.25 and 0.33, -72: for higher performance, increase the cut-off and the PME grid spacing. -72: -72: -72: -72: There were 3 NOTEs -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'UNNAMED in water' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 42 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.029 0.007 394.4 -72: (ns/day) (hour/ns) -72: Performance: 58.152 0.413 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to -816517429 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2211 of the 2211 non-bonded parameter combinations -72: -72: Generated 2211 of the 2211 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -72: -72: turning H bonds into constraints... -72: -72: NOTE 2 [file ala.top, line 256]: -72: For energy conservation with LINCS, lincs_iter should be 2 or larger. -72: -72: -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -72: Number of degrees of freedom in T-Coupling group rest is 54.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 -72: Calculating fourier grid dimensions for X Y Z -72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: -72: The optimal PME mesh load for parallel simulations is below 0.5 -72: and for highly parallel simulations between 0.25 and 0.33, -72: for higher performance, increase the cut-off and the PME grid spacing. -72: -72: -72: -72: There were 3 NOTEs -72: -72: Estimate for the relative computational load of the PME mesh part: 0.94 -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -72: Can not increase nstlist because an NVE ensemble is used -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'UNNAMED in water' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 44 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.034 0.009 392.7 -72: (ns/day) (hour/ns) -72: Performance: 49.897 0.481 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -72: -72: -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 -72: -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (43 ms) -72: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (411 ms total) -72: -72: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest -72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to 764245870 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -72: Pull group 1 'FirstWaterMolecule' has 3 atoms -72: Pull group 2 'SecondWaterMolecule' has 3 atoms -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: Pull group natoms pbc atom distance at start reference at t=0 -72: 1 3 2 -72: 2 3 5 1.112 nm 1.000 nm -72: -72: This run will generate roughly 0 Mb of data -72: -72: There was 1 NOTE -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 47 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.035 0.009 394.7 -72: (ns/day) (hour/ns) -72: Performance: 48.758 0.492 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: Setting the LD random seed to -88087049 -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2.gro' -72: Pull group 1 'FirstWaterMolecule' has 3 atoms -72: Pull group 2 'SecondWaterMolecule' has 3 atoms -72: Number of degrees of freedom in T-Coupling group rest is 9.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: Pull group natoms pbc atom distance at start reference at t=0 -72: 1 3 2 -72: 2 3 5 1.112 nm 1.000 nm -72: -72: This run will generate roughly 0 Mb of data -72: -72: There was 1 NOTE -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. -72: Can not increase nstlist because an NVE ensemble is used -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 4 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 48 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.044 0.011 395.8 -72: (ns/day) (hour/ns) -72: Performance: 38.689 0.620 -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSi Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 ngleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 -72: -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 -72: -72: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file -72: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file -72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (38 ms) -72: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (38 ms total) -72: -72: [----------] 12 tests from FreezeWorks/FreezeGroupTest -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: NVE simulation: will use the initial temperature of 246.451 K for -72: determining the Verlet buffer size -72: -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: This run will generate roughly 0 Mb of data -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 5 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.3%. -72: The balanceable part of the MD step is 43%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.1%. -72: -72: -72: NOTE: 46 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.043 0.011 397.1 -72: (ns/day) (hour/ns) -72: Performance: 71.957 0.334 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (26 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: NVE simulation: will use the initial temperature of 246.451 K for -72: determining the Verlet buffer size -72: -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: This run will generate roughly 0 Mb of data -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 5 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 3.8%. -72: The balanceable part of the MD step is 49%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 1.8%. -72: -72: -72: NOTE: 46 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.052 0.013 397.3 -72: (ns/day) (hour/ns) -72: Performance: 59.499 0.403 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (27 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: NVE simulation: will use the initial temperature of 246.451 K for -72: determining the Verlet buffer size -72: -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: This run will generate roughly 0 Mb of data -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 5 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 3.5%. -72: The balanceable part of the MD step is 47%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 1.6%. -72: -72: -72: NOTE: 44 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.028 0.007 395.4 -72: (ns/day) (hour/ns) -72: Performance: 108.326 0.222 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (22 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: NVE simulation: will use the initial temperature of 246.451 K for -72: determining the Verlet buffer size -72: -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 5 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 3.8%. -72: The balanceable part of the MD step is 53%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 2.0%. -72: -72: -72: NOTE: 44 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.025 0.006 392.7 -72: -72: (ns/day) (hour/ns) -72: Performance: 122.809 0.195 -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (20 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: NVE simulation: will use the initial temperature of 246.451 K for -72: determining the Verlet buffer size -72: -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 5 NOTEs -72: -72: There was 1 WARNING -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 3.4%. -72: The balanceable part of the MD step is 51%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 1.7%. -72: -72: -72: NOTE: 47 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.047 0.012 398.2 -72: (ns/day) (hour/ns) -72: Performance: 65.690 0.365 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (27 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -72: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: This run will generate roughly 0 Mb of data -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.028 0.007 397.4 -72: (ns/day) (hour/ns) -72: Performance: 112.158 0.214 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (19 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.028 0.007 397.3 -72: (ns/day) (hour/ns) -72: Performance: 111.727 0.215 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (19 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vacuo.gro' -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.026 0.006 397.0 -72: (ns/day) (hour/ns) -72: Performance: 119.765 0.200 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (18 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 46 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.028 0.007 397.3 -72: (ns/day) (hour/ns) -72: Performance: 109.310 0.220 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (34 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.023 0.006 396.6 -72: (ns/day) (hour/ns) -72: Performance: 134.027 0.179 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (33 ms) -72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Generated 2145 of the 2145 non-bonded parameter combinations -72: -72: Generated 2145 of the 2145 1-4 parameter combinations -72: -72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' -72: -72: turning H bonds into constraints... -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -72: There are 5 atoms that are fully frozen and part of COMM removal -72: group(s), removing these atoms from the COMM removal group(s) -72: -72: -72: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -72: There are 3 atoms that are frozen along less then 3 dimensions and part -72: of COMM removal group(s), due to limitations in the code these still -72: contribute to the mass of the COM along frozen dimensions and therefore -72: the COMM correction will be too small. -72: -72: Number of degrees of freedom in T-Coupling group System is 33.00 -72: -72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -72: -72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm -72: -72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm -72: -72: Note that mdrun will redetermine rlist based on the actual pair-list setup -72: -72: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: -72: You are using a plain Coulomb cut-off, which might produce artifacts. -72: You might want to consider using PME electrostatics. -72: -72: -72: -72: There were 4 NOTEs -72: -72: There was 1 WARNING -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 -72: -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'Alanine-dipeptide' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: NOTE: 47 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.039 0.010 398.1 -72: (ns/day) (hour/ns) -72: Performance: 79.510 0.302 -72: -72: -72: -72: -72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (37 ms) -72: [----------] 12 tests from FreezeWorks/FreezeGroupTest (287 ms total) -72: -72: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest -72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: Net Acceleration in X direction, will not be corrected -72: Net Acceleration in Y direction, will not be corrected -72: Net Acceleration in Z direction, will not be corrected -72: -72: There were 3 NOTEs -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Setting gen_seed to -126386689 -72: -72: Velocities were taken from a Maxwell distribution at 0 K -72: -72: This run will generate roughly 0 Mb of data -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.6%. -72: The balanceable part of the MD step is 44%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.3%. -72: -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.024 0.006 393.4 -72: -72: (ns/day) (hour/ns) -72: Performance: 251.619 0.095 -72: -72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (12 ms) -72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Setting gen_seed to 966696955 -72: -72: Velocities were taken from a Maxwell distribution at 0 K -72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -72: Net Acceleration in X direction, will not be corrected -72: Net Acceleration in Y direction, will not be corrected -72: Net Acceleration in Z direction, will not be corrected -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because verlet-buffer-tolerance is not set or used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.1%. -72: The balanceable part of the MD step is 44%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.0%. -72: -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: -72: Time: 0.026 0.007 395.8 -72: (ns/day) (hour/ns) -72: Performance: 232.847 0.103 -72: -72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (13 ms) -72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generating 1-4 interactions: fudge = 0.5 -72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -72: Net Acceleration in X direction, will not be corrected -72: Net Acceleration in Y direction, will not be corrected -72: Net Acceleration in Z direction, will not be corrected -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because an NVE ensemble is used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 8 steps, 0.0 ps. -72: Generated 3 of the 3 non-bonded parameter combinations -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Setting gen_seed to -1749551362 -72: -72: Velocities were taken from a Maxwell distribution at 0 K -72: -72: This run will generate roughly 0 Mb of data -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.2%. -72: The balanceable part of the MD step is 45%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.1%. -72: -72: -72: NOTE: 44 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: Time: 0.027 0.007 395.6 -72: (ns/day) (hour/ns) -72: Performance: 230.706 0.104 -72: -72: -72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (12 ms) -72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 -72: -72: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -72: that with the Verlet scheme, nstlist has no effect on the accuracy of -72: your simulation. -72: -72: -72: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance -72: < 0 -72: -72: -72: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: -72: Setting nstcalcenergy (100) equal to nstenergy (4) -72: -72: Generated 3 of the 3 non-bonded parameter combinations -72: Generating 1-4 interactions: fudge = 0.5 -72: -72: Generated 3 of the 3 1-4 parameter combinations -72: -72: Excluding 2 bonded neighbours molecule type 'SOL' -72: -72: Setting gen_seed to -1077938689 -72: -72: Velocities were taken from a Maxwell distribution at 0 K -72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 -72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 -72: Net Acceleration in X direction, will not be corrected -72: Net Acceleration in Y direction, will not be corrected -72: Net Acceleration in Z direction, will not be corrected -72: -72: This run will generate roughly 0 Mb of data -72: -72: There were 3 NOTEs -72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -72: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -72: Can not increase nstlist because verlet-buffer-tolerance is not set or used -72: Using 2 MPI processes -72: Using 2 OpenMP threads per MPI process -72: -72: -72: NOTE: The number of threads is not equal to the number of (logical) cpus -72: and the -pin option is set to auto: will not pin threads to cpus. -72: This can lead to significant performance degradation. -72: Consider using -pin on (and -pinoffset in case you run multiple jobs). -72: starting mdrun 'spc2' -72: 8 steps, 0.0 ps. -72: -72: Writing final coordinates. -72: -72: -72: Dynamic load balancing report: -72: DLB was off during the run due to low measured imbalance. -72: Average load imbalance: 0.1%. -72: The balanceable part of the MD step is 48%, load imbalance is computed from this. -72: Part of the total run time spent waiting due to load imbalance: 0.1%. -72: -72: -72: NOTE: 45 % of the run time was spent communicating energies, -72: you might want to increase some nst* mdp options -72: -72: Core t (s) Wall t (s) (%) -72: -72: Time: 0.029 0.007 395.8 -72: (ns/day) (hour/ns) -72: Performance: 215.921 0.111 -72: -72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (14 ms) -72: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (54 ms total) -72: -72: [----------] Global test environment tear-down -72: [==========] 29 tests from 8 test suites ran. (2179 ms total) -72: [ PASSED ] 28 tests. -72: [ SKIPPED ] 1 test, listed below: -72: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 -72/96 Test #72: MdrunTestsTwoRanks ........................... Passed 2.45 sec -test 73 - Start 73: MdrunSingleRankAlgorithmsTests - -73: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" -73: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -73: Test timeout computed to be: 600 -73: [==========] Running 5 tests from 3 test suites. -73: [----------] Global test environment set-up. -73: [----------] 1 test from DispersionCorrectionTest -73: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 30.00 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -73: There are 9 non-linear virtual site constructions. Their contribution to -73: the energy error is approximated. In most cases this does not affect the -73: error significantly. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: There were 2 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 -73: -73: Update groups can not be used for this system because an incompatible virtual site type is used -73: -73: Using 1 MPI process -73: Using 2 OpenMP threads -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: starting mdrun 'Alanine dipeptide in vacuo' -73: 200 steps, 0.4 ps. -73: Setting the LD random seed to 938999279 -73: -73: Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -73: -73: turning H bonds into constraints... -73: -73: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -73: -73: Cleaning up constraints and constant bonded interactions with virtual sites -73: -73: Converted 3 Bonds with virtual sites to connections, 7 left -73: -73: Removed 18 Angles with virtual sites, 21 left -73: -73: Removed 10 Proper Dih.s with virtual sites, 44 left -73: -73: Converted 12 Constraints with virtual sites to connections, 0 left -73: -73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -73: -73: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm -73: -73: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm -73: -73: Note that mdrun will redetermine rlist based on the actual pair-list setup -73: -73: This run will generate roughly 0 Mb of data -73: -73: Writing final coordinates. -73: -73: Core t (s) Wall t (s) (%) -73: Time: 0.029 0.014 199.3 -73: (ns/day) (hour/ns) -73: Performance: 2419.771 0.010 -73: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (37 ms) -73: [----------] 1 test from DispersionCorrectionTest (37 ms total) -73: -73: [----------] 1 test from OriresTest -73: [ RUN ] OriresTest.OriresCanRun -73: Generating 1-4 interactions: fudge = 0.5 -73: Number of degrees of freedom in T-Coupling group System is 518.00 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: -73: You are using a plain Coulomb cut-off, which might produce artifacts. -73: You might want to consider using PME electrostatics. -73: -73: -73: -73: There was 1 NOTE -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 -73: -73: Using 1 MPI process -73: Using 2 OpenMP threads -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' -73: 10 steps, 0.0 ps. -73: Setting the LD random seed to -287314018 -73: -73: Generated 2145 of the 2145 non-bonded parameter combinations -73: -73: Generated 2145 of the 2145 1-4 parameter combinations -73: -73: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -73: -73: turning H bonds into constraints... -73: -73: Excluding 2 bonded neighbours molecule type 'SOL' -73: -73: turning H bonds into constraints... -73: -73: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/orires_1lvz.gro' -73: -73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K -73: -73: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm -73: -73: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm -73: -73: Note that mdrun will redetermine rlist based on the actual pair-list setup -73: -73: This run will generate roughly 0 Mb of data -73: -73: Writing final coordinates. -73: -73: Core t (s) Wall t (s) (%) -73: Time: 2.499 1.250 200.0 -73: (ns/day) (hour/ns) -73: Performance: 1.521 15.777 -73: [ OK ] OriresTest.OriresCanRun (1564 ms) -73: [----------] 1 test from OriresTest (1564 ms total) -73: -73: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest -73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 -73: Number of degrees of freedom in T-Coupling group rest is 10.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -73: NVE simulation with an initial temperature of zero: will use a Verlet -73: buffer of 10%. Check your energy drift! -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: -73: The optimal PME mesh load for parallel simulations is below 0.5 -73: and for highly parallel simulations between 0.25 and 0.33, -73: for higher performance, increase the cut-off and the PME grid spacing. -73: -73: -73: -73: There were 2 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Can not increase nstlist because an NVE ensemble is used -73: Using 1 MPI process -73: Using 2 OpenMP threads -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: starting mdrun 'Dipoles' -73: 20 steps, 0.1 ps. -73: Setting the LD random seed to -87031879 -73: -73: Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Dipole' -73: -73: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -73: -73: Searching the wall atom type(s) -73: -73: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -73: Calculating fourier grid dimensions for X Y Z -73: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 -73: -73: Estimate for the relative computational load of the PME mesh part: 1.00 -73: -73: This run will generate roughly 0 Mb of data -73: -73: Writing final coordinates. -73: -73: Core t (s) Wall t (s) (%) -73: Time: 2.348 1.174 200.0 -73: (ns/day) (hour/ns) -73: Performance: 3.864 6.211 -73: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) -73: -73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (1877 ms) -73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 -73: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. -73: The supported numbers are > 1. -73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) -73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 -73: -73: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -73: With epsilon_surface > 0 all molecules should be neutral. -73: -73: -73: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -73: With epsilon_surface > 0 you can only use domain decomposition when there -73: are only small molecules with all bonds constrained (mdrun will check for -73: this). -73: -73: Number of degrees of freedom in T-Coupling group rest is 9.00 -73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -73: -73: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -73: NVE simulation with an initial temperature of zero: will use a Verlet -73: buffer of 10%. Check your energy drift! -73: -73: -73: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: -73: The optimal PME mesh load for parallel simulations is below 0.5 -73: and for highly parallel simulations between 0.25 and 0.33, -73: for higher performance, increase the cut-off and the PME grid spacing. -73: -73: -73: -73: There were 4 NOTEs -73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -73: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -73: Can not increase nstlist because an NVE ensemble is used -73: Using 1 MPI process -73: Using 2 OpenMP threads -73: -73: -73: NOTE: The number of threads is not equal to the number of (logical) cpus -73: and the -pin option is set to auto: will not pin threads to cpus. -73: This can lead to significant performance degradation. -73: Consider using -pin on (and -pinoffset in case you run multiple jobs). -73: starting mdrun 'Dipoles' -73: 20 steps, 0.1 ps. -73: Setting the LD random seed to -348192769 -73: -73: Generated 1 of the 1 non-bonded parameter combinations -73: -73: Excluding 1 bonded neighbours molecule type 'Dipole' -73: -73: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero -73: -73: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 -73: Calculating fourier grid dimensions for X Y Z -73: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 -73: -73: Estimate for the relative computational load of the PME mesh part: 1.00 -73: -73: This run will generate roughly 0 Mb of data -73: -73: Writing final coordinates. -73: -73: Core t (s) Wall t (s) (%) -73: Time: 1.926 0.963 200.0 -73: (ns/day) (hour/ns) -73: Performance: 4.710 5.095 -73: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file -73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 -73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (1189 ms) -73: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (3066 ms total) -73: -73: [----------] Global test environment tear-down -73: [==========] 5 tests from 3 test suites ran. (4743 ms total) -73: [ PASSED ] 5 tests. -73/96 Test #73: MdrunSingleRankAlgorithmsTests ............... Passed 4.94 sec -test 74 - Start 74: Minimize1RankTests - -74: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/Minimize1RankTests.xml" -74: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -74: Test timeout computed to be: 600 -74: [==========] Running 12 tests from 2 test suites. -74: [----------] Global test environment set-up. -74: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Steepest Descents: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Steepest Descents did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = -4.7991062e+01 -74: Maximum force = 1.8629750e+02 on atom 13 -74: Norm of force = 8.7721970e+01 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (232 ms) -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 330891 of the 330891 non-bonded parameter combinations -74: Generating 1-4 interactions: fudge = 0.5 -74: -74: Generated 330891 of the 330891 1-4 parameter combinations -74: -74: Excluding 2 bonded neighbours molecule type 'SOL' -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Polak-Ribiere Conjugate Gradients: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: F-max = 3.02330e+02 on atom 3 -74: F-Norm = 1.18024e+02 -74: -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = -5.5862370e+01 -74: Maximum force = 4.2727301e+02 on atom 13 -74: Norm of force = 1.8452934e+02 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (212 ms) -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 1 -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Glycine' -74: -74: turning H bonds into constraints... -74: Number of degrees of freedom in T-Coupling group System is 22.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Steepest Descents: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Steepest Descents did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = 3.1937723e+02 -74: Maximum force = 9.9988623e+03 on atom 9 -74: Norm of force = 4.6166987e+03 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (52 ms) -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: Generating 1-4 interactions: fudge = 1 -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Glycine' -74: -74: turning H bonds into constraints... -74: -74: NOTE 3 [file glycine_vacuo.top, line 12]: -74: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -74: -74: Number of degrees of freedom in T-Coupling group System is 22.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 5 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Polak-Ribiere Conjugate Gradients: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: F-max = 2.41575e+04 on atom 10 -74: F-Norm = 1.18451e+04 -74: -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = 1.5174393e+02 -74: Maximum force = 7.4208867e+03 on atom 9 -74: Norm of force = 3.5693011e+03 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (51 ms) -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 5 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Steepest Descents: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Steepest Descents did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = -1.5698462e+02 -74: Maximum force = 4.5704999e+02 on atom 17 -74: Norm of force = 1.8327331e+02 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (9 ms) -74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generating 1-4 interactions: fudge = 0.5 -74: Generated 2145 of the 2145 non-bonded parameter combinations -74: -74: Generated 2145 of the 2145 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -74: -74: turning all bonds into constraints... -74: -74: NOTE 3 [file unknown]: -74: You are using constraints on all bonds, whereas the forcefield has been -74: parametrized only with constraints involving hydrogen atoms. We suggest -74: using constraints = h-bonds instead, this will also improve performance. -74: -74: -74: NOTE 4 [file unknown]: -74: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -74: -74: -74: Cleaning up constraints and constant bonded interactions with virtual sites -74: -74: Removed 18 Angles with virtual sites, 21 left -74: -74: Removed 10 Proper Dih.s with virtual sites, 44 left -74: -74: Converted 15 Constraints with virtual sites to connections, 7 left -74: Number of degrees of freedom in T-Coupling group System is 23.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 6 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Update groups can not be used for this system because an incompatible virtual site type is used -74: -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Polak-Ribiere Conjugate Gradients: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: F-max = 1.06799e+03 on atom 28 -74: F-Norm = 4.26916e+02 -74: -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = -1.6941089e+02 -74: Maximum force = 2.1831544e+02 on atom 17 -74: Norm of force = 7.9209568e+01 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (9 ms) -74: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (568 ms total) -74: -74: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 3 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Steepest Descents: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: -74: writing lowest energy coordinates. -74: -74: Steepest Descents converged to Fmax < 10 in 1 steps -74: Potential Energy = -9.7425687e-01 -74: Maximum force = 4.0132279e+00 on atom 1 -74: Norm of force = 1.6383933e+00 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (4 ms) -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_Energy -74: This run will generate roughly 0 Mb of data -74: MinimizationTest_WithinTolerances_1_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 3 NOTEs -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Polak-Ribiere Conjugate Gradients: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: F-max = 4.01323e+00 on atom 1 -74: F-Norm = 1.63839e+00 -74: -74: -74: writing lowest energy coordinates. -74: -74: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -74: Potential Energy = -9.9064195e-01 -74: Maximum force = 2.5781672e+00 on atom 1 -74: Norm of force = 1.0525324e+00 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (4 ms) -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: -74: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -74: -74: Generated 1 of the 1 non-bonded parameter combinations -74: -74: Excluding 1 bonded neighbours molecule type 'Argon' -74: Number of degrees of freedom in T-Coupling group System is 33.00 -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 3 NOTEs -74: -74: There was 1 WARNING -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Low-Memory BFGS Minimizer: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: Using 10 BFGS correction steps. -74: -74: F-max = 4.01323e+00 on atom 1 -74: F-Norm = 1.63839e+00 -74: -74: -74: writing lowest energy coordinates. -74: -74: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps -74: Potential Energy = -9.9064195e-01 -74: Maximum force = 2.5781672e+00 on atom 1 -74: Norm of force = 1.0525324e+00 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: Generating 1-4 interactions: fudge = 1 -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Glycine' -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Steepest Descents: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Steepest Descents did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = 3.1939685e+02 -74: Maximum force = 9.9704248e+03 on atom 9 -74: Norm of force = 4.6227543e+03 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (53 ms) -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: Generating 1-4 interactions: fudge = 1 -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Glycine' -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Polak-Ribiere Conjugate Gradients: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: F-max = 2.41672e+04 on atom 10 -74: F-Norm = 1.19357e+04 -74: -74: -74: Energy minimization reached the maximum number of steps before the forces -74: reached the requested precision Fmax < 10. -74: -74: writing lowest energy coordinates. -74: -74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -74: Potential Energy = 1.5625757e+02 -74: Maximum force = 7.5018242e+03 on atom 9 -74: Norm of force = 3.6139019e+03 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (51 ms) -74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -74: -74: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -74: that with the Verlet scheme, nstlist has no effect on the accuracy of -74: your simulation. -74: -74: -74: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -74: setting nstcomm equal to nstcalcenergy for less overhead -74: -74: -74: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -74: -74: Generating 1-4 interactions: fudge = 1 -74: Generated 20503 of the 20503 non-bonded parameter combinations -74: -74: Generated 17396 of the 20503 1-4 parameter combinations -74: -74: Excluding 3 bonded neighbours molecule type 'Glycine' -74: Number of degrees of freedom in T-Coupling group System is 27.00 -74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -74: -74: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: You are using a plain Coulomb cut-off, which might produce artifacts. -74: You might want to consider using PME electrostatics. -74: -74: -74: -74: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -74: COM removal frequency is set to (4). -74: Other settings require a global communication frequency of 100. -74: Note that this will require additional global communication steps, -74: which will reduce performance when using multiple ranks. -74: Consider setting nstcomm to a multiple of 100. -74: -74: -74: There were 4 NOTEs -74: -74: There was 1 WARNING -74: -74: This run will generate roughly 0 Mb of data -74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -74: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -74: Using 1 MPI process -74: Using 2 OpenMP threads -74: -74: -74: NOTE: The number of threads is not equal to the number of (logical) cpus -74: and the -pin option is set to auto: will not pin threads to cpus. -74: This can lead to significant performance degradation. -74: Consider using -pin on (and -pinoffset in case you run multiple jobs). -74: -74: Low-Memory BFGS Minimizer: -74: Tolerance (Fmax) = 1.00000e+01 -74: Number of steps = 4 -74: Using 10 BFGS correction steps. -74: -74: F-max = 2.41672e+04 on atom 10 -74: F-Norm = 1.19357e+04 -74: -74: -74: Energy minimization has stopped, but the forces have not converged to the -74: requested precision Fmax < 10 (which may not be possible for your system). It -74: stopped because the algorithm tried to make a new step whose size was too -74: small, or there was no change in the energy since last step. Either way, we -74: regard the minimization as converged to within the available machine -74: precision, given your starting configuration and EM parameters. -74: -74: Double precision normally gives you higher accuracy, but this is often not -74: needed for preparing to run molecular dynamics. -74: -74: writing lowest energy coordinates. -74: -74: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, -74: but did not reach the requested Fmax < 10. -74: Potential Energy = 5.6111725e+02 -74: Maximum force = 1.2685490e+04 on atom 10 -74: Norm of force = 6.0643616e+03 -74: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (49 ms) -74: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (168 ms total) -74: -74: [----------] Global test environment tear-down -74: [==========] 12 tests from 2 test suites ran. (775 ms total) -74: [ PASSED ] 12 tests. -74/96 Test #74: Minimize1RankTests ........................... Passed 1.18 sec -test 75 - Start 75: Minimize2RankTests - -75: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/Minimize2RankTests.xml" -75: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -75: Test timeout computed to be: 600 -75: [==========] Running 12 tests from 2 test suites. -75: [----------] Global test environment set-up. -75: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generated 330891 of the 330891 non-bonded parameter combinations -75: Generating 1-4 interactions: fudge = 0.5 -75: -75: Generated 330891 of the 330891 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: Number of degrees of freedom in T-Coupling group System is 27.00 -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: This run will generate roughly 0 Mb of data -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Steepest Descents: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Steepest Descents did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = -4.7990963e+01 -75: Maximum force = 1.8629601e+02 on atom 13 -75: Norm of force = 8.7721907e+01 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (260 ms) -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generated 330891 of the 330891 non-bonded parameter combinations -75: Generating 1-4 interactions: fudge = 0.5 -75: -75: Generated 330891 of the 330891 1-4 parameter combinations -75: -75: Excluding 2 bonded neighbours molecule type 'SOL' -75: Number of degrees of freedom in T-Coupling group System is 27.00 -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Polak-Ribiere Conjugate Gradients: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: F-max = 3.02331e+02 on atom 3 -75: F-Norm = 1.18024e+02 -75: -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = -5.5862366e+01 -75: Maximum force = 4.2726111e+02 on atom 13 -75: Norm of force = 1.8452509e+02 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (209 ms) -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generated 20503 of the 20503 non-bonded parameter combinations -75: Generating 1-4 interactions: fudge = 1 -75: -75: Generated 17396 of the 20503 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Glycine' -75: -75: turning H bonds into constraints... -75: Number of degrees of freedom in T-Coupling group System is 22.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Steepest Descents: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Steepest Descents did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = 3.1937720e+02 -75: Maximum force = 9.9988643e+03 on atom 9 -75: Norm of force = 4.6166993e+03 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (51 ms) -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generating 1-4 interactions: fudge = 1 -75: Generated 20503 of the 20503 non-bonded parameter combinations -75: -75: Generated 17396 of the 20503 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Glycine' -75: -75: turning H bonds into constraints... -75: -75: NOTE 3 [file glycine_vacuo.top, line 12]: -75: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -75: -75: Number of degrees of freedom in T-Coupling group System is 22.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 5 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Polak-Ribiere Conjugate Gradients: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: F-max = 2.41575e+04 on atom 10 -75: F-Norm = 1.18451e+04 -75: -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = 1.5174432e+02 -75: Maximum force = 7.4208867e+03 on atom 9 -75: Norm of force = 3.5692995e+03 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (50 ms) -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generating 1-4 interactions: fudge = 0.5 -75: Generated 2145 of the 2145 non-bonded parameter combinations -75: -75: Generated 2145 of the 2145 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -75: -75: turning all bonds into constraints... -75: -75: NOTE 3 [file unknown]: -75: You are using constraints on all bonds, whereas the forcefield has been -75: parametrized only with constraints involving hydrogen atoms. We suggest -75: using constraints = h-bonds instead, this will also improve performance. -75: -75: -75: Cleaning up constraints and constant bonded interactions with virtual sites -75: -75: Removed 18 Angles with virtual sites, 21 left -75: -75: Removed 10 Proper Dih.s with virtual sites, 44 left -75: -75: Converted 15 Constraints with virtual sites to connections, 7 left -75: Number of degrees of freedom in T-Coupling group System is 23.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 5 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Update groups can not be used for this system because an incompatible virtual site type is used -75: -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Steepest Descents: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Steepest Descents did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = -1.5698450e+02 -75: Maximum force = 4.5703549e+02 on atom 17 -75: Norm of force = 1.8327631e+02 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (10 ms) -75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generating 1-4 interactions: fudge = 0.5 -75: Generated 2145 of the 2145 non-bonded parameter combinations -75: -75: Generated 2145 of the 2145 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -75: -75: turning all bonds into constraints... -75: -75: NOTE 3 [file unknown]: -75: You are using constraints on all bonds, whereas the forcefield has been -75: parametrized only with constraints involving hydrogen atoms. We suggest -75: using constraints = h-bonds instead, this will also improve performance. -75: -75: -75: NOTE 4 [file unknown]: -75: For accurate cg with LINCS constraints, lincs-order should be 8 or more. -75: -75: -75: Cleaning up constraints and constant bonded interactions with virtual sites -75: -75: Removed 18 Angles with virtual sites, 21 left -75: -75: Removed 10 Proper Dih.s with virtual sites, 44 left -75: -75: Converted 15 Constraints with virtual sites to connections, 7 left -75: Number of degrees of freedom in T-Coupling group System is 23.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 6 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Update groups can not be used for this system because an incompatible virtual site type is used -75: -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Polak-Ribiere Conjugate Gradients: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: F-max = 1.06799e+03 on atom 28 -75: F-Norm = 4.26916e+02 -75: -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = -1.6941107e+02 -75: Maximum force = 2.1831662e+02 on atom 17 -75: Norm of force = 7.9213110e+01 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (10 ms) -75: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (593 ms total) -75: -75: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 -75: Generated 1 of the 1 non-bonded parameter combinations -75: Number of degrees of freedom in T-Coupling group System is 33.00 -75: -75: Excluding 1 bonded neighbours molecule type 'Argon' -75: -75: This run will generate roughly 0 Mb of data -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 3 NOTEs -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Steepest Descents: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: -75: writing lowest energy coordinates. -75: -75: Steepest Descents converged to Fmax < 10 in 1 steps -75: Potential Energy = -9.7425687e-01 -75: Maximum force = 4.0132279e+00 on atom 3 -75: Norm of force = 1.6383933e+00 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (6 ms) -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generated 1 of the 1 non-bonded parameter combinations -75: -75: Excluding 1 bonded neighbours molecule type 'Argon' -75: Number of degrees of freedom in T-Coupling group System is 33.00 -75: -75: This run will generate roughly 0 Mb of data -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 3 NOTEs -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Polak-Ribiere Conjugate Gradients: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: F-max = 4.01323e+00 on atom 3 -75: F-Norm = 1.63839e+00 -75: -75: -75: writing lowest energy coordinates. -75: -75: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps -75: Potential Energy = -9.9064195e-01 -75: Maximum force = 2.5781672e+00 on atom 3 -75: Norm of force = 1.0525324e+00 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (7 ms) -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: -75: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -75: -75: Generated 1 of the 1 non-bonded parameter combinations -75: -75: Excluding 1 bonded neighbours molecule type 'Argon' -75: Number of degrees of freedom in T-Coupling group System is 33.00 -75: -75: This run will generate roughly 0 Mb of data -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 3 NOTEs -75: -75: There was 1 WARNING -75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3 ms) -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generating 1-4 interactions: fudge = 1 -75: Generated 20503 of the 20503 non-bonded parameter combinations -75: -75: Generated 17396 of the 20503 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Glycine' -75: Number of degrees of freedom in T-Coupling group System is 27.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Steepest Descents: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Steepest Descents did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = 3.1939673e+02 -75: Maximum force = 9.9704229e+03 on atom 9 -75: Norm of force = 4.6227558e+03 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (63 ms) -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: Generated 20503 of the 20503 non-bonded parameter combinations -75: Generating 1-4 interactions: fudge = 1 -75: -75: Generated 17396 of the 20503 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Glycine' -75: Number of degrees of freedom in T-Coupling group System is 27.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: -75: This run will generate roughly 0 Mb of data -75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -75: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -75: Using 2 MPI processes -75: Using 2 OpenMP threads per MPI process -75: -75: -75: NOTE: The number of threads is not equal to the number of (logical) cpus -75: and the -pin option is set to auto: will not pin threads to cpus. -75: This can lead to significant performance degradation. -75: Consider using -pin on (and -pinoffset in case you run multiple jobs). -75: -75: Polak-Ribiere Conjugate Gradients: -75: Tolerance (Fmax) = 1.00000e+01 -75: Number of steps = 4 -75: F-max = 2.41672e+04 on atom 10 -75: F-Norm = 1.19357e+04 -75: -75: -75: Energy minimization reached the maximum number of steps before the forces -75: reached the requested precision Fmax < 10. -75: -75: writing lowest energy coordinates. -75: -75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. -75: Potential Energy = 1.5625764e+02 -75: Maximum force = 7.5018237e+03 on atom 9 -75: Norm of force = 3.6139019e+03 -75: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file -75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (50 ms) -75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 -75: -75: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -75: that with the Verlet scheme, nstlist has no effect on the accuracy of -75: your simulation. -75: -75: -75: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -75: setting nstcomm equal to nstcalcenergy for less overhead -75: -75: -75: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. -75: -75: Generated 20503 of the 20503 non-bonded parameter combinations -75: Generating 1-4 interactions: fudge = 1 -75: -75: Generated 17396 of the 20503 1-4 parameter combinations -75: -75: Excluding 3 bonded neighbours molecule type 'Glycine' -75: Number of degrees of freedom in T-Coupling group System is 27.00 -75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -75: -75: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: You are using a plain Coulomb cut-off, which might produce artifacts. -75: You might want to consider using PME electrostatics. -75: -75: -75: -75: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: -75: COM removal frequency is set to (4). -75: Other settings require a global communication frequency of 100. -75: Note that this will require additional global communication steps, -75: which will reduce performance when using multiple ranks. -75: Consider setting nstcomm to a multiple of 100. -75: -75: -75: There were 4 NOTEs -75: -75: There was 1 WARNING -75: -75: This run will generate roughly 0 Mb of data -75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (47 ms) -75: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (179 ms total) -75: -75: [----------] Global test environment tear-down -75: [==========] 12 tests from 2 test suites ran. (834 ms total) -75: [ PASSED ] 12 tests. -75/96 Test #75: Minimize2RankTests ........................... Passed 1.11 sec -test 76 - Start 76: MdrunNonIntegratorTests - -76: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" -76: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -76: Test timeout computed to be: 600 -76: [==========] Running 46 tests from 3 test suites. -76: [----------] Global test environment set-up. -76: [----------] 1 test from NonbondedBenchTest -76: [ RUN ] NonbondedBenchTest.BasicEndToEndTest -76: SIMD width: 4 -76: System size: 3000 atoms -76: Cut-off radius: 1 nm -76: Number of threads: 1 -76: Number of iterations: 1 -76: Compute energies: no -76: Ewald excl. corr.: analytical -76: -76: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle -76: total useful -76: Ewald all geom. 4xM 10.346 10.3456 0.1151 0.0609 -76: [ OK ] NonbondedBenchTest.BasicEndToEndTest (15 ms) -76: [----------] 1 test from NonbondedBenchTest (15 ms total) -76: -76: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Number of degrees of freedom in T-Coupling group System is 33.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: -76: NVE simulation: will use the initial temperature of 68.810 K for -76: determining the Verlet buffer size -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Argon' -76: 16 steps, 0.0 ps. -76: Generated 1 of the 1 non-bonded parameter combinations -76: -76: Excluding 1 bonded neighbours molecule type 'Argon' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 3.318 1.659 200.0 -76: (ns/day) (hour/ns) -76: Performance: 0.885 27.111 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' -76: -76: trr version: GMX_trn_file (single precision) -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 23 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 194.4 -76: (ns/day) (hour/ns) -76: Performance: 1949.555 0.012 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (1792 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Number of degrees of freedom in T-Coupling group System is 33.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: -76: NVE simulation: will use the initial temperature of 68.810 K for -76: determining the Verlet buffer size -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Argon' -76: 16 steps, 0.0 ps. -76: Generated 1 of the 1 non-bonded parameter combinations -76: -76: Excluding 1 bonded neighbours molecule type 'Argon' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.918 0.459 200.0 -76: (ns/day) (hour/ns) -76: Performance: 3.201 7.497 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 180.7 -76: (ns/day) (hour/ns) -76: Performance: 2322.999 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (532 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Number of degrees of freedom in T-Coupling group System is 33.00 -76: -76: There were 2 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Argon' -76: 16 steps, 0.0 ps. -76: Generated 1 of the 1 non-bonded parameter combinations -76: -76: Excluding 1 bonded neighbours molecule type 'Argon' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.981 0.490 200.0 -76: (ns/day) (hour/ns) -76: Performance: 2.995 8.012 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 24 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 193.2 -76: (ns/day) (hour/ns) -76: Performance: 2366.728 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (592 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Number of degrees of freedom in T-Coupling group System is 33.00 -76: -76: There were 2 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Argon' -76: 16 steps, 0.0 ps. -76: Generated 1 of the 1 non-bonded parameter combinations -76: -76: Excluding 1 bonded neighbours molecule type 'Argon' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 1.303 0.651 200.0 -76: (ns/day) (hour/ns) -76: Performance: 2.255 10.643 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 24 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 192.9 -76: (ns/day) (hour/ns) -76: Performance: 2412.135 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (824 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 27.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -76: NVE simulation: will use the initial temperature of 398.997 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 16 steps, 0.0 ps. -76: Generated 330891 of the 330891 non-bonded parameter combinations -76: -76: Generated 330891 of the 330891 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.325 0.163 199.9 -76: (ns/day) (hour/ns) -76: Performance: 9.036 2.656 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 22 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 192.6 -76: (ns/day) (hour/ns) -76: Performance: 2379.526 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (390 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 27.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -76: NVE simulation: will use the initial temperature of 398.997 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 16 steps, 0.0 ps. -76: Generated 330891 of the 330891 non-bonded parameter combinations -76: -76: Generated 330891 of the 330891 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.019 0.010 199.3 -76: (ns/day) (hour/ns) -76: Performance: 150.995 0.159 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 192.5 -76: (ns/day) (hour/ns) -76: Performance: 2418.765 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (223 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 27.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 16 steps, 0.0 ps. -76: Generated 330891 of the 330891 non-bonded parameter combinations -76: -76: Generated 330891 of the 330891 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.615 0.307 200.0 -76: (ns/day) (hour/ns) -76: Performance: 4.777 5.024 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 29 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 193.7 -76: (ns/day) (hour/ns) -76: Performance: 2037.907 0.012 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (527 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 27.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'spc2' -76: 16 steps, 0.0 ps. -76: Generated 330891 of the 330891 non-bonded parameter combinations -76: -76: Generated 330891 of the 330891 1-4 parameter combinations -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.9 -76: (ns/day) (hour/ns) -76: Performance: 145.338 0.165 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.001 0.001 192.1 -76: (ns/day) (hour/ns) -76: Performance: 2334.442 0.010 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (224 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: -76: NOTE 3 [file unknown]: -76: You are using constraints on all bonds, whereas the forcefield has been -76: parametrized only with constraints involving hydrogen atoms. We suggest -76: using constraints = h-bonds instead, this will also improve performance. -76: -76: Number of degrees of freedom in T-Coupling group System is 23.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -76: NVE simulation: will use the initial temperature of 456.887 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -76: There are 9 non-linear virtual site constructions. Their contribution to -76: the energy error is approximated. In most cases this does not affect the -76: error significantly. -76: -76: -76: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 6 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Alanine dipeptide in vacuo' -76: 16 steps, 0.0 ps. -76: Generated 2145 of the 2145 non-bonded parameter combinations -76: -76: Generated 2145 of the 2145 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -76: -76: turning all bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -76: -76: Cleaning up constraints and constant bonded interactions with virtual sites -76: -76: Removed 18 Angles with virtual sites, 21 left -76: -76: Removed 10 Proper Dih.s with virtual sites, 44 left -76: -76: Converted 15 Constraints with virtual sites to connections, 7 left -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.8 -76: (ns/day) (hour/ns) -76: Performance: 143.373 0.167 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 22 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 194.0 -76: (ns/day) (hour/ns) -76: Performance: 1645.458 0.015 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (25 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: -76: NOTE 3 [file unknown]: -76: You are using constraints on all bonds, whereas the forcefield has been -76: parametrized only with constraints involving hydrogen atoms. We suggest -76: using constraints = h-bonds instead, this will also improve performance. -76: -76: Number of degrees of freedom in T-Coupling group System is 23.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -76: NVE simulation: will use the initial temperature of 456.887 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -76: There are 9 non-linear virtual site constructions. Their contribution to -76: the energy error is approximated. In most cases this does not affect the -76: error significantly. -76: -76: -76: NOTE 6 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 6 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Alanine dipeptide in vacuo' -76: 16 steps, 0.0 ps. -76: Generated 2145 of the 2145 non-bonded parameter combinations -76: -76: Generated 2145 of the 2145 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -76: -76: turning all bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -76: -76: Cleaning up constraints and constant bonded interactions with virtual sites -76: -76: Removed 18 Angles with virtual sites, 21 left -76: -76: Removed 10 Proper Dih.s with virtual sites, 44 left -76: -76: Converted 15 Constraints with virtual sites to connections, 7 left -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.014 0.007 198.5 -76: (ns/day) (hour/ns) -76: Performance: 207.232 0.116 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 194.5 -76: (ns/day) (hour/ns) -76: Performance: 1633.676 0.015 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (21 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: -76: NOTE 3 [file unknown]: -76: You are using constraints on all bonds, whereas the forcefield has been -76: parametrized only with constraints involving hydrogen atoms. We suggest -76: using constraints = h-bonds instead, this will also improve performance. -76: -76: Number of degrees of freedom in T-Coupling group System is 23.00 -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -76: There are 9 non-linear virtual site constructions. Their contribution to -76: the energy error is approximated. In most cases this does not affect the -76: error significantly. -76: -76: -76: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 5 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 -76: -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Alanine dipeptide in vacuo' -76: 16 steps, 0.0 ps. -76: Generated 2145 of the 2145 non-bonded parameter combinations -76: -76: Generated 2145 of the 2145 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -76: -76: turning all bonds into constraints... -76: -76: Cleaning up constraints and constant bonded interactions with virtual sites -76: -76: Removed 18 Angles with virtual sites, 21 left -76: -76: Removed 10 Proper Dih.s with virtual sites, 44 left -76: -76: Converted 15 Constraints with virtual sites to connections, 7 left -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.017 0.009 198.6 -76: (ns/day) (hour/ns) -76: Performance: 170.990 0.140 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 -76: -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 22 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 193.1 -76: (ns/day) (hour/ns) -76: Performance: 1512.916 0.016 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (78 ms) -76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: -76: NOTE 3 [file unknown]: -76: You are using constraints on all bonds, whereas the forcefield has been -76: parametrized only with constraints involving hydrogen atoms. We suggest -76: using constraints = h-bonds instead, this will also improve performance. -76: -76: Number of degrees of freedom in T-Coupling group System is 23.00 -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -76: There are 9 non-linear virtual site constructions. Their contribution to -76: the energy error is approximated. In most cases this does not affect the -76: error significantly. -76: -76: -76: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 5 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 -76: -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun 'Alanine dipeptide in vacuo' -76: 16 steps, 0.0 ps. -76: Generated 2145 of the 2145 non-bonded parameter combinations -76: -76: Generated 2145 of the 2145 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' -76: -76: turning all bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' -76: -76: Cleaning up constraints and constant bonded interactions with virtual sites -76: -76: Removed 18 Angles with virtual sites, 21 left -76: -76: Removed 10 Proper Dih.s with virtual sites, 44 left -76: -76: Converted 15 Constraints with virtual sites to connections, 7 left -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.018 0.009 198.9 -76: (ns/day) (hour/ns) -76: Performance: 166.633 0.144 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 -76: -76: Update groups can not be used for this system because an incompatible virtual site type is used -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 23 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 193.2 -76: (ns/day) (hour/ns) -76: Performance: 1616.529 0.015 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (44 ms) -76: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (5279 ms total) -76: -76: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.3 -76: (ns/day) (hour/ns) -76: Performance: 146.730 0.164 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.4 -76: (ns/day) (hour/ns) -76: Performance: 1460.549 0.016 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (24 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.6 -76: (ns/day) (hour/ns) -76: Performance: 149.518 0.161 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.1 -76: (ns/day) (hour/ns) -76: Performance: 1345.695 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (24 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.029 0.015 199.0 -76: (ns/day) (hour/ns) -76: Performance: 101.161 0.237 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.2 -76: (ns/day) (hour/ns) -76: Performance: 1358.755 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (29 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.022 0.011 199.1 -76: (ns/day) (hour/ns) -76: Performance: 134.470 0.178 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.7 -76: (ns/day) (hour/ns) -76: Performance: 1400.453 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (25 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.018 0.009 198.8 -76: (ns/day) (hour/ns) -76: Performance: 165.163 0.145 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.6 -76: (ns/day) (hour/ns) -76: Performance: 1333.462 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (22 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.017 0.009 198.8 -76: (ns/day) (hour/ns) -76: Performance: 171.237 0.140 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 182.6 -76: (ns/day) (hour/ns) -76: Performance: 1353.084 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (22 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.035 0.017 199.3 -76: (ns/day) (hour/ns) -76: Performance: 84.863 0.283 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 14 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.003 0.002 189.2 -76: (ns/day) (hour/ns) -76: Performance: 922.245 0.026 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (36 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.021 0.010 199.0 -76: (ns/day) (hour/ns) -76: Performance: 141.178 0.170 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 14 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 125.7 -76: (ns/day) (hour/ns) -76: Performance: 1005.647 0.024 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (26 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.027 0.014 198.8 -76: (ns/day) (hour/ns) -76: Performance: 108.075 0.222 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 185.1 -76: (ns/day) (hour/ns) -76: Performance: 1349.528 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (27 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.018 0.009 198.4 -76: (ns/day) (hour/ns) -76: Performance: 161.306 0.149 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.5 -76: (ns/day) (hour/ns) -76: Performance: 1338.677 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (24 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.5 -76: (ns/day) (hour/ns) -76: Performance: 144.972 0.166 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 10 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.002 97.1 -76: (ns/day) (hour/ns) -76: Performance: 727.686 0.033 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (25 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.031 0.016 199.7 -76: (ns/day) (hour/ns) -76: Performance: 94.627 0.254 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.5 -76: (ns/day) (hour/ns) -76: Performance: 1441.749 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (30 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.029 0.015 199.7 -76: (ns/day) (hour/ns) -76: Performance: 100.404 0.239 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 16 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 160.5 -76: (ns/day) (hour/ns) -76: Performance: 1168.993 0.021 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (29 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.028 0.014 199.6 -76: (ns/day) (hour/ns) -76: Performance: 103.485 0.232 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 179.8 -76: (ns/day) (hour/ns) -76: Performance: 1360.555 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (27 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.026 0.013 199.7 -76: (ns/day) (hour/ns) -76: Performance: 111.942 0.214 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.8 -76: (ns/day) (hour/ns) -76: Performance: 1405.245 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (27 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.024 0.012 199.6 -76: (ns/day) (hour/ns) -76: Performance: 122.998 0.195 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.0 -76: (ns/day) (hour/ns) -76: Performance: 1291.258 0.019 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (26 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.022 0.011 199.6 -76: (ns/day) (hour/ns) -76: Performance: 134.784 0.178 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.8 -76: (ns/day) (hour/ns) -76: Performance: 1443.438 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (24 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.029 0.014 199.7 -76: (ns/day) (hour/ns) -76: Performance: 102.227 0.235 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.4 -76: (ns/day) (hour/ns) -76: Performance: 1371.154 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (28 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.023 0.011 199.6 -76: (ns/day) (hour/ns) -76: Performance: 128.407 0.187 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.1 -76: (ns/day) (hour/ns) -76: Performance: 1395.062 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (25 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.028 0.014 199.6 -76: (ns/day) (hour/ns) -76: Performance: 105.241 0.228 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.003 54.4 -76: (ns/day) (hour/ns) -76: Performance: 437.139 0.055 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (32 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.026 0.013 199.7 -76: (ns/day) (hour/ns) -76: Performance: 112.757 0.213 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.4 -76: (ns/day) (hour/ns) -76: Performance: 1501.119 0.016 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (27 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -76: NVE simulation: will use the initial temperature of 294.908 K for -76: determining the Verlet buffer size -76: -76: -76: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 4 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.041 0.021 199.8 -76: (ns/day) (hour/ns) -76: Performance: 71.573 0.335 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Can not increase nstlist because an NVE ensemble is used -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.7 -76: (ns/day) (hour/ns) -76: Performance: 1394.430 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (42 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 198.5 -76: (ns/day) (hour/ns) -76: Performance: 143.333 0.167 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.6 -76: (ns/day) (hour/ns) -76: Performance: 1362.360 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (32 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.024 0.012 199.2 -76: (ns/day) (hour/ns) -76: Performance: 121.444 0.198 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 185.0 -76: (ns/day) (hour/ns) -76: Performance: 1379.443 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (34 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.026 0.013 199.3 -76: (ns/day) (hour/ns) -76: Performance: 111.242 0.216 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.1 -76: (ns/day) (hour/ns) -76: Performance: 1395.378 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (37 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.021 0.011 199.1 -76: (ns/day) (hour/ns) -76: Performance: 137.470 0.175 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.9 -76: (ns/day) (hour/ns) -76: Performance: 1316.366 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (33 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.018 0.009 198.9 -76: (ns/day) (hour/ns) -76: Performance: 159.407 0.151 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.8 -76: (ns/day) (hour/ns) -76: Performance: 1353.679 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (35 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.017 0.009 198.8 -76: (ns/day) (hour/ns) -76: Performance: 170.597 0.141 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 19 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.8 -76: (ns/day) (hour/ns) -76: Performance: 1356.959 0.018 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (32 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.022 0.011 199.2 -76: (ns/day) (hour/ns) -76: Performance: 130.463 0.184 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 184.0 -76: (ns/day) (hour/ns) -76: Performance: 1444.792 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (33 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.021 0.011 199.1 -76: (ns/day) (hour/ns) -76: Performance: 138.615 0.173 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 22 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 183.1 -76: (ns/day) (hour/ns) -76: Performance: 1380.061 0.017 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (34 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.017 0.009 198.4 -76: (ns/day) (hour/ns) -76: Performance: 167.731 0.143 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 187.2 -76: (ns/day) (hour/ns) -76: Performance: 1766.732 0.014 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (29 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.021 0.010 199.1 -76: (ns/day) (hour/ns) -76: Performance: 141.405 0.170 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 21 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 186.9 -76: (ns/day) (hour/ns) -76: Performance: 1773.854 0.014 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (31 ms) -76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 -76: -76: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -76: that with the Verlet scheme, nstlist has no effect on the accuracy of -76: your simulation. -76: -76: -76: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -76: Setting nstcalcenergy (100) equal to nstenergy (4) -76: -76: Generating 1-4 interactions: fudge = 0.5 -76: Number of degrees of freedom in T-Coupling group System is 79.00 -76: -76: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: -76: You are using a plain Coulomb cut-off, which might produce artifacts. -76: You might want to consider using PME electrostatics. -76: -76: -76: -76: There were 3 NOTEs -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting mdrun '30 atom system in water' -76: 16 steps, 0.0 ps. -76: Generated 2485 of the 2485 non-bonded parameter combinations -76: -76: Generated 2485 of the 2485 1-4 parameter combinations -76: -76: Excluding 3 bonded neighbours molecule type 'nonanol' -76: -76: turning H bonds into constraints... -76: -76: Excluding 2 bonded neighbours molecule type 'SOL' -76: -76: turning H bonds into constraints... -76: -76: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -76: -76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -76: -76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -76: -76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -76: -76: Note that mdrun will redetermine rlist based on the actual pair-list setup -76: -76: This run will generate roughly 0 Mb of data -76: -76: Writing final coordinates. -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.020 0.010 199.1 -76: (ns/day) (hour/ns) -76: Performance: 143.835 0.167 -76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -76: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -76: -76: Using 1 MPI process -76: Using 2 OpenMP threads -76: -76: -76: NOTE: The number of threads is not equal to the number of (logical) cpus -76: and the -pin option is set to auto: will not pin threads to cpus. -76: This can lead to significant performance degradation. -76: Consider using -pin on (and -pinoffset in case you run multiple jobs). -76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' -76: -76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 -76: -76: NOTE: 20 % of the run time was spent in pair search, -76: you might want to increase nstlist (this has no effect on accuracy) -76: -76: Core t (s) Wall t (s) (%) -76: Time: 0.002 0.001 185.9 -76: (ns/day) (hour/ns) -76: Performance: 1727.108 0.014 -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file -76: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file -76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 -76: -76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (30 ms) -76: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (977 ms total) -76: -76: [----------] Global test environment tear-down -76: [==========] 46 tests from 3 test suites ran. (6324 ms total) -76: [ PASSED ] 46 tests. -76/96 Test #76: MdrunNonIntegratorTests ...................... Passed 6.52 sec -test 77 - Start 77: MdrunTpiTests - -77: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunTpiTests.xml" -77: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -77: Test timeout computed to be: 600 -77: [==========] Running 3 tests from 1 test suite. -77: [----------] Global test environment set-up. -77: [----------] 3 tests from Simple/TpiTest -77: [ RUN ] Simple/TpiTest.ReproducesOutput/0 -77: Generating 1-4 interactions: fudge = 0.5 -77: Number of degrees of freedom in T-Coupling group System is 1308.00 -77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -77: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -77: TPI is not implemented for GPUs. -77: -77: Using 1 MPI process -77: Using 1 OpenMP thread -77: -77: -77: NOTE: Thread affinity was not set. -77: Reading frames from gro file '216 water molecules', 648 atoms. -77: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 -77: Last frame 0 time 0.000 -77: Generated 331705 of the 331705 non-bonded parameter combinations -77: -77: Generated 331705 of the 331705 1-4 parameter combinations -77: -77: Excluding 2 bonded neighbours molecule type 'SOL' -77: -77: Excluding 3 bonded neighbours molecule type 'methane' -77: Analysing residue names: -77: There are: 216 Water residues -77: There are: 1 Other residues -77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -77: -77: This run will generate roughly 0 Mb of data -77: [ OK ] Simple/TpiTest.ReproducesOutput/0 (232 ms) -77: [ RUN ] Simple/TpiTest.ReproducesOutput/1 -77: Generating 1-4 interactions: fudge = 0.5 -77: Number of degrees of freedom in T-Coupling group System is 1308.00 -77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -77: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -77: TPI is not implemented for GPUs. -77: -77: Using 1 MPI process -77: Using 1 OpenMP thread -77: -77: -77: NOTE: Thread affinity was not set. -77: Reading frames from gro file '216 water molecules', 648 atoms. -77: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 -77: Last frame 0 time 0.000 -77: Generated 331705 of the 331705 non-bonded parameter combinations -77: -77: Generated 331705 of the 331705 1-4 parameter combinations -77: -77: Excluding 2 bonded neighbours molecule type 'SOL' -77: -77: Excluding 3 bonded neighbours molecule type 'methane' -77: Analysing residue names: -77: There are: 216 Water residues -77: There are: 1 Other residues -77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -77: -77: This run will generate roughly 0 Mb of data -77: [ OK ] Simple/TpiTest.ReproducesOutput/1 (216 ms) -77: [ RUN ] Simple/TpiTest.ReproducesOutput/2 -77: Generating 1-4 interactions: fudge = 0.5 -77: Number of degrees of freedom in T-Coupling group System is 1308.00 -77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -77: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -77: TPI is not implemented for GPUs. -77: -77: Using 1 MPI process -77: Using 1 OpenMP thread -77: -77: -77: NOTE: Thread affinity was not set. -77: Reading frames from gro file '216 water molecules', 648 atoms. -77: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 -77: Last frame 0 time 0.000 -77: Generated 331705 of the 331705 non-bonded parameter combinations -77: -77: Generated 331705 of the 331705 1-4 parameter combinations -77: -77: Excluding 2 bonded neighbours molecule type 'SOL' -77: -77: Excluding 3 bonded neighbours molecule type 'methane' -77: Analysing residue names: -77: There are: 216 Water residues -77: There are: 1 Other residues -77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... -77: -77: This run will generate roughly 0 Mb of data -77: [ OK ] Simple/TpiTest.ReproducesOutput/2 (219 ms) -77: [----------] 3 tests from Simple/TpiTest (669 ms total) -77: -77: [----------] Global test environment tear-down -77: [==========] 3 tests from 1 test suite ran. (691 ms total) -77: [ PASSED ] 3 tests. -77/96 Test #77: MdrunTpiTests ................................ Passed 0.88 sec -test 78 - Start 78: MdrunMpiTests - -78: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMpiTests.xml" -78: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -78: Test timeout computed to be: 600 -78: [==========] Running 16 tests from 2 test suites. -78: [----------] Global test environment set-up. -78: [----------] 4 tests from MimicTest -78: [ RUN ] MimicTest.OneQuantumMol -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -78: For a correct single-point energy evaluation with nsteps = 0, use -78: continuation = yes to avoid constraining the input coordinates. -78: -78: Setting the LD random seed to 1543363310 -78: -78: Generated 10 of the 10 non-bonded parameter combinations -78: -78: Generated 10 of the 10 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group rest is 21.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -78: NVE simulation with an initial temperature of zero: will use a Verlet -78: buffer of 10%. Check your energy drift! -78: -78: -78: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: -78: You are using a plain Coulomb cut-off, which might produce artifacts. -78: You might want to consider using PME electrostatics. -78: -78: -78: -78: This run will generate roughly 0 Mb of data -78: -78: There were 3 NOTEs -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -78: -78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -78: Reading frame 0 time 0.000 Last frame 0 time 0.000 -78: -78: NOTE: 20 % of the run time was spent in domain decomposition, -78: 16 % of the run time was spent in pair search, -78: you might want to increase nstlist (this has no effect on accuracy) -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.002 0.000 377.8 -78: (ns/day) (hour/ns) -78: Performance: 208.809 0.115 -78: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file -78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (9 ms) -78: [ RUN ] MimicTest.AllQuantumMol -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -78: For a correct single-point energy evaluation with nsteps = 0, use -78: continuation = yes to avoid constraining the input coordinates. -78: -78: Setting the LD random seed to -41961617 -78: -78: Generated 10 of the 10 non-bonded parameter combinations -78: -78: Generated 10 of the 10 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group rest is 21.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -78: NVE simulation with an initial temperature of zero: will use a Verlet -78: buffer of 10%. Check your energy drift! -78: -78: -78: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: -78: You are using a plain Coulomb cut-off, which might produce artifacts. -78: You might want to consider using PME electrostatics. -78: -78: -78: -78: This run will generate roughly 0 Mb of data -78: -78: There were 3 NOTEs -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -78: -78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -78: Reading frame 0 time 0.000 Last frame 0 time 0.000 -78: -78: NOTE: 22 % of the run time was spent in domain decomposition, -78: 14 % of the run time was spent in pair search, -78: you might want to increase nstlist (this has no effect on accuracy) -78: -78: NOTE: 5 % of the run time was spent communicating energies, -78: you might want to increase some nst* mdp options -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.001 0.000 378.5 -78: (ns/day) (hour/ns) -78: Performance: 246.187 0.097 -78: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file -78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (6 ms) -78: [ RUN ] MimicTest.TwoQuantumMol -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -78: For a correct single-point energy evaluation with nsteps = 0, use -78: continuation = yes to avoid constraining the input coordinates. -78: -78: Setting the LD random seed to -604116225 -78: -78: Generated 10 of the 10 non-bonded parameter combinations -78: -78: Generated 10 of the 10 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group rest is 21.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -78: NVE simulation with an initial temperature of zero: will use a Verlet -78: buffer of 10%. Check your energy drift! -78: -78: -78: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: -78: You are using a plain Coulomb cut-off, which might produce artifacts. -78: You might want to consider using PME electrostatics. -78: -78: -78: -78: This run will generate roughly 0 Mb of data -78: -78: There were 3 NOTEs -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/4water.gro' -78: -78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. -78: Reading frame 0 time 0.000 Last frame 0 time 0.000 -78: -78: NOTE: 23 % of the run time was spent in domain decomposition, -78: 14 % of the run time was spent in pair search, -78: you might want to increase nstlist (this has no effect on accuracy) -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.001 0.000 377.9 -78: (ns/day) (hour/ns) -78: Performance: 250.354 0.096 -78: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file -78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (6 ms) -78: [ RUN ] MimicTest.BondCuts -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -78: For a correct single-point energy evaluation with nsteps = 0, use -78: continuation = yes to avoid constraining the input coordinates. -78: -78: Setting the LD random seed to -1078542793 -78: -78: Generated 2211 of the 2211 non-bonded parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Generated 2211 of the 2211 1-4 parameter combinations -78: -78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -78: Number of degrees of freedom in T-Coupling group rest is 66.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -78: NVE simulation: will use the initial temperature of 300.368 K for -78: determining the Verlet buffer size -78: -78: -78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K -78: -78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm -78: -78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm -78: -78: Note that mdrun will redetermine rlist based on the actual pair-list setup -78: -78: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: -78: You are using a plain Coulomb cut-off, which might produce artifacts. -78: You might want to consider using PME electrostatics. -78: -78: -78: -78: This run will generate roughly 0 Mb of data -78: -78: There were 3 NOTEs -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/ala.gro' -78: -78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. -78: Reading frame 0 time 0.000 Last frame 0 time 0.000 -78: -78: NOTE: 18 % of the run time was spent in domain decomposition, -78: 16 % of the run time was spent in pair search, -78: you might want to increase nstlist (this has no effect on accuracy) -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.002 0.000 383.0 -78: (ns/day) (hour/ns) -78: Performance: 182.196 0.132 -78: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file -78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (15 ms) -78: [----------] 4 tests from MimicTest (38 ms total) -78: -78: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest -78: Setting the LD random seed to -1626374181 -78: -78: Generated 3 of the 3 non-bonded parameter combinations -78: -78: Generated 3 of the 3 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group rest is 9.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -78: NVE simulation with an initial temperature of zero: will use a Verlet -78: buffer of 10%. Check your energy drift! -78: -78: -78: There was 1 NOTE -78: -78: This run will generate roughly 0 Mb of data -78: Setting the LD random seed to 1459092892 -78: -78: Generated 3 of the 3 non-bonded parameter combinations -78: -78: Generated 3 of the 3 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group System is 9.00 -78: -78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -78: -78: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm -78: -78: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm -78: -78: Note that mdrun will redetermine rlist based on the actual pair-list setup -78: -78: This run will generate roughly 0 Mb of data -78: Generating 1-4 interactions: fudge = 0.5 -78: Setting the LD random seed to -339739713 -78: -78: Generated 3 of the 3 non-bonded parameter combinations -78: -78: Generated 3 of the 3 1-4 parameter combinations -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group rest is 9.00 -78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -78: NVE simulation with an initial temperature of zero: will use a Verlet -78: buffer of 10%. Check your energy drift! -78: -78: -78: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -78: The optimal PME mesh load for parallel simulations is below 0.5 -78: and for highly parallel simulations between 0.25 and 0.33, -78: for higher performance, increase the cut-off and the PME grid spacing. -78: -78: -78: -78: There were 2 NOTEs -78: -78: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -78: Calculating fourier grid dimensions for X Y Z -78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -78: -78: Estimate for the relative computational load of the PME mesh part: 1.00 -78: -78: This run will generate roughly 0 Mb of data -78: Setting the LD random seed to -672202791 -78: -78: Generated 3 of the 3 non-bonded parameter combinations -78: -78: Generated 3 of the 3 1-4 parameter combinations -78: Generating 1-4 interactions: fudge = 0.5 -78: -78: Excluding 2 bonded neighbours molecule type 'SOL' -78: -78: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero -78: Number of degrees of freedom in T-Coupling group System is 9.00 -78: -78: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 -78: -78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -78: -78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -78: -78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -78: -78: Note that mdrun will redetermine rlist based on the actual pair-list setup -78: Calculating fourier grid dimensions for X Y Z -78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -78: -78: Estimate for the relative computational load of the PME mesh part: 1.00 -78: -78: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: -78: The optimal PME mesh load for parallel simulations is below 0.5 -78: and for highly parallel simulations between 0.25 and 0.33, -78: for higher performance, increase the cut-off and the PME grid spacing. -78: -78: -78: -78: There was 1 NOTE -78: -78: This run will generate roughly 0 Mb of data -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: -78: Dynamic load balancing report: -78: DLB was off during the run due to low measured imbalance. -78: Average load imbalance: 1.3%. -78: The balanceable part of the MD step is 54%, load imbalance is computed from this. -78: Part of the total run time spent waiting due to load imbalance: 0.7%. -78: -78: -78: NOTE: 46 % of the run time was spent communicating energies, -78: you might want to increase some nst* mdp options -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.057 0.014 398.4 -78: (ns/day) (hour/ns) -78: Performance: 126.833 0.189 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (17 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 -78: -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: NOTE: 40 % of the run time was spent communicating energies, -78: you might want to increase some nst* mdp options -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.020 0.005 395.0 -78: (ns/day) (hour/ns) -78: Performance: 354.405 0.068 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (8 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: -78: Dynamic load balancing report: -78: DLB was off during the run due to low measured imbalance. -78: Average load imbalance: 6.1%. -78: The balanceable part of the MD step is 7%, load imbalance is computed from this. -78: Part of the total run time spent waiting due to load imbalance: 0.4%. -78: -78: -78: NOTE: 21 % of the run time was spent communicating energies, -78: you might want to increase some nst* mdp options -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.046 0.012 398.6 -78: (ns/day) (hour/ns) -78: Performance: 155.582 0.154 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (158 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Can not increase nstlist because an NVE ensemble is used -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: Core t (s) Wall t (s) (%) -78: Time: 1.158 0.290 399.8 -78: (ns/day) (hour/ns) -78: Performance: 6.263 3.832 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (376 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Changing nstlist from 10 to 100, rlist from 1 to 1 -78: -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: NOTE: 28 % of the run time was spent communicating energies, -78: you might want to increase some nst* mdp options -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.061 0.015 398.0 -78: (ns/day) (hour/ns) -78: Performance: 118.812 0.202 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (28 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -78: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -78: Changing nstlist from 10 to 100, rlist from 1 to 1 -78: -78: Using 2 MPI processes -78: Using 2 OpenMP threads per MPI process -78: -78: -78: NOTE: The number of threads is not equal to the number of (logical) cpus -78: and the -pin option is set to auto: will not pin threads to cpus. -78: This can lead to significant performance degradation. -78: Consider using -pin on (and -pinoffset in case you run multiple jobs). -78: starting mdrun 'spc2' -78: 20 steps, 0.0 ps. -78: -78: Writing final coordinates. -78: -78: Core t (s) Wall t (s) (%) -78: Time: 0.056 0.014 398.2 -78: (ns/day) (hour/ns) -78: Performance: 129.846 0.185 -78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (26 ms) -78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) -78: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (617 ms total) -78: -78: [----------] Global test environment tear-down -78: [==========] 16 tests from 2 test suites ran. (731 ms total) -78: [ PASSED ] 10 tests. -78: [ SKIPPED ] 6 tests, listed below: -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 -78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 -78/96 Test #78: MdrunMpiTests ................................ Passed 1.00 sec -test 79 - Start 79: MdrunMultiSimTests - -79: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" -79: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -79: Test timeout computed to be: 600 -79: [==========] Running 6 tests from 2 test suites. -79: [----------] Global test environment set-up. -79: [----------] 4 tests from InNvt/MultiSimTest -79: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 -79: Setting the LD random seed to -277030290 -79: Setting the LD random seed to -1345359873 -79: Setting the LD random seed to -41948996 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: Setting the LD random seed to -1342310057 -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Setting gen_seed to -4198417 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: -79: Setting gen_seed to -567377 -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Setting gen_seed to 1031779452 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Velocities were taken from a Maxwell distribution at 288 K -79: -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: This run will generate roughly 0 Mb of data -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: There were 2 NOTEs -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -472121873 -79: -79: Velocities were taken from a Maxwell distribution at 268 K -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: This run will generate roughly 0 Mb of data -79: -79: There were 2 NOTEs -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: This is simulation 3 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 2 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 0 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 1 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (18 ms) -79: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -135792129 -79: Setting the LD random seed to 995555070 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Generated 3 of the 3 1-4 parameter combinations -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -201719810 -79: -79: Setting gen_seed to 1727790886 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: There were 2 NOTEs -79: -79: This run will generate roughly 0 Mb of data -79: -79: This run will generate roughly 0 Mb of data -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: This is simulation 0 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: This is simulation 1 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: Using 1 OpenMP thread per MPI process -79: -79: Using 1 OpenMP thread per MPI process -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: -79: Writing final coordinates. -79: -79: NOTE: 47 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: -79: Writing final coordinates. -79: -79: NOTE: 47 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (12 ms) -79: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: For a correct single-point energy evaluation with nsteps = 0, use -79: continuation = yes to avoid constraining the input coordinates. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -1042881237 -79: Setting the LD random seed to -1888616457 -79: Setting the LD random seed to -573064777 -79: Setting the LD random seed to -358618129 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to 490667007 -79: -79: Velocities were taken from a Maxwell distribution at 288 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to 1855972303 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -136446210 -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -1610620929 -79: -79: Velocities were taken from a Maxwell distribution at 268 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 3 NOTEs -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: This run will generate roughly 0 Mb of data -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: This is simulation 0 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 2 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 3 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 1 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: Using 1 OpenMP thread Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 0 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 1 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 2 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 3 steps, 0.0 ps. -79: -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: -79: NOTE: 15 % of the run time was spent in pair search, -79: you might want to increase nstlist (this has no effect on accuracy) -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (10 ms) -79: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: -79: For a correct single-point energy evaluation with nsteps = 0, use -79: continuation = yes to avoid constraining the input coordinates. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to 662517759 -79: Setting the LD random seed to -1055745 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -538978306 -79: -79: Setting gen_seed to -269484305 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 3 NOTEs -79: This run will generate roughly 0 Mb of data -79: This run will generate roughly 0 Mb of data -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: This is simulation 0 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: This is simulation 1 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: Using 1 OpenMP thread per MPI process -79: -79: Using 1 OpenMP thread per MPI process -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 1 steps, 0.0 ps. -79: starting mdrun 'spc2' -79: 0 steps, 0.0 ps. -79: -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Note: The number of steps is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: NOTE: 30 % of the run time was spent in domain decomposition, -79: 15 % of the run time was spent in pair search, -79: you might want to increase nstlist (this has no effect on accuracy) -79: -79: Writing final coordinates. -79: -79: NOTE: 48 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (6 ms) -79: [----------] 4 tests from InNvt/MultiSimTest (61 ms total) -79: -79: [----------] 2 tests from InNvt/MultiSimTerminationTest -79: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -808532075 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Setting the LD random seed to -294293002 -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Setting gen_seed to -204112001 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: Setting gen_seed to -147000341 -79: -79: Velocities were taken from a Maxwell distribution at 288 K -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: This run will generate roughly 0 Mb of data -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: There were 2 NOTEs -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -419906309 -79: Setting the LD random seed to -791693337 -79: Generating 1-4 interactions: fudge = 0.5 -79: Generating 1-4 interactions: fudge = 0.5 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -1077420034 -79: -79: Velocities were taken from a Maxwell distribution at 268 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -318769409 -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: This is simulation 0 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 1 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 2 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: This is simulation 3 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: -79: Step 8: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: -79: Step 7: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: -79: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: -79: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 -79: -79: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 -79: -79: -79: This is simulation 0 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: -79: This is simulation 1 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: -79: This is simulation 2 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: Using 1 OpenMP thread -79: -79: -79: This is simulation 3 out of 4 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 1 MPI process -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: Using 1 OpenMP thread -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 11 steps, 0.0 ps (continuing from step 9, 0.0 ps). -79: starting mdrun 'spc2' -79: 10 steps, 0.0 ps (continuing from step 8, 0.0 ps). -79: starting mdrun 'spc2' -79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). -79: starting mdrun 'spc2' -79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). -79: -79: -79: Note: The initial step is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Note: The initial step is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Note: The initial step is not consistent across multi simulations, -79: but we are proceeding anyway! -79: Note: The initial step is not consistent across multi simulations, -79: but we are proceeding anyway! -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (27 ms) -79: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -1382813697 -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to 1029912139 -79: -79: Velocities were taken from a Maxwell distribution at 298 K -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: This run will generate roughly 0 Mb of data -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: -79: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: -79: You have set rlist larger than the interaction cut-off, but you also have -79: verlet-buffer-tolerance > 0. Will set rlist using -79: verlet-buffer-tolerance. -79: -79: Setting the LD random seed to -271060997 -79: -79: Generated 3 of the 3 non-bonded parameter combinations -79: -79: Generated 3 of the 3 1-4 parameter combinations -79: Generating 1-4 interactions: fudge = 0.5 -79: -79: Excluding 2 bonded neighbours molecule type 'SOL' -79: -79: Setting gen_seed to -16896282 -79: -79: Velocities were taken from a Maxwell distribution at 278 K -79: Number of degrees of freedom in T-Coupling group System is 9.00 -79: -79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -79: -79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -79: -79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -79: -79: Note that mdrun will redetermine rlist based on the actual pair-list setup -79: -79: -79: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: -79: You are using a plain Coulomb cut-off, which might produce artifacts. -79: You might want to consider using PME electrostatics. -79: -79: -79: -79: There were 2 NOTEs -79: This run will generate roughly 0 Mb of data -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -79: -79: This is simulation 0 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: This is simulation 1 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: Using 1 OpenMP thread per MPI process -79: -79: Using 1 OpenMP thread per MPI process -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: starting mdrun 'spc2' -79: 100 steps, 0.1 ps. -79: -79: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: -79: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps -79: -79: -79: Dynamic load balancing report: -79: DLB was off during the run due to low measured imbalance. -79: Average load imbalance: 34.0%. -79: The balanceable part of the MD step is 3%, load imbalance is computed from this. -79: Part of the total run time spent waiting due to load imbalance: 1.1%. -79: -79: -79: NOTE: 43 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: -79: -79: Dynamic load balancing report: -79: DLB was off during the run due to low measured imbalance. -79: Average load imbalance: 0.2%. -79: The balanceable part of the MD step is 3%, load imbalance is computed from this. -79: Part of the total run time spent waiting due to load imbalance: 0.0%. -79: -79: -79: NOTE: 43 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -79: -79: -79: This is simulation 0 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: -79: This is simulation 1 out of 2 running as a composite GROMACS -79: multi-simulation job. Setup for this simulation: -79: -79: Using 2 MPI processes -79: Using 1 OpenMP thread per MPI process -79: -79: Using 1 OpenMP thread per MPI process -79: -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: -79: NOTE: The number of threads is not equal to the number of (logical) cpus -79: and the -pin option is set to auto: will not pin threads to cpus. -79: This can lead to significant performance degradation. -79: Consider using -pin on (and -pinoffset in case you run multiple jobs). -79: starting mdrun 'spc2' -79: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). -79: starting mdrun 'spc2' -79: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). -79: -79: Writing final coordinates. -79: -79: Writing final coordinates. -79: -79: NOTE: 47 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: -79: NOTE: 47 % of the run time was spent communicating energies, -79: you might want to increase some nst* mdp options -79: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (20 ms) -79: [----------] 2 tests from InNvt/MultiSimTerminationTest (49 ms total) -79: -79: [----------] Global test environment tear-down -79: [==========] 6 tests from 2 test suites ran. (204 ms total) -79: [ PASSED ] 6 tests. -79/96 Test #79: MdrunMultiSimTests ........................... Passed 0.47 sec -test 80 - Start 80: MdrunMultiSimReplexTests - -80: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" -80: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -80: Test timeout computed to be: 600 -80: [==========] Running 5 tests from 2 test suites. -80: [----------] Global test environment set-up. -80: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest -80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: Setting the LD random seed to 1877473535 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -37783686 -80: -80: Velocities were taken from a Maxwell distribution at 278 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: Setting the LD random seed to -35672577 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: This run will generate roughly 0 Mb of data -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: -80: Setting gen_seed to -72368137 -80: -80: Velocities were taken from a Maxwell distribution at 268 K -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: Setting the LD random seed to -8566929 -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: -80: There were 2 NOTEs -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: Setting the LD random seed to 2079702775 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -41419165 -80: -80: Velocities were taken from a Maxwell distribution at 288 K -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -1093935699 -80: -80: Velocities were taken from a Maxwell distribution at 298 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: This is simulation 0 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: This is simulation 3 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 1 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 2 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: 2 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (21 ms) -80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: Setting the LD random seed to -18889005 -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -423625320 -80: -80: Velocities were taken from a Maxwell distribution at 288 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: Setting the LD random seed to -1392706065 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: Setting the LD random seed to -110142480 -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -1085409605 -80: -80: Velocities were taken from a Maxwell distribution at 278 K -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: Setting gen_seed to 2126996478 -80: -80: Velocities were taken from a Maxwell distribution at 268 K -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: Setting the LD random seed to 1034903149 -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -134349032 -80: -80: Velocities were taken from a Maxwell distribution at 298 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: This run will generate roughly 0 Mb of data -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: This is simulation 1 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 2 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: This is simulation 0 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: This is simulation 3 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (15 ms) -80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: Setting the LD random seed to -547094657 -80: Setting the LD random seed to -344080902 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to 1037024738 -80: -80: Setting gen_seed to -1077969716 -80: -80: -80: Velocities were taken from a Maxwell distribution at 298 K -80: Velocities were taken from a Maxwell distribution at 278 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: -80: This run will generate roughly 0 Mb of data -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There were 2 NOTEs -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: This is simulation 0 out of 2 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 2 MPI processes -80: This is simulation 1 out of 2 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 2 MPI processes -80: Using 1 OpenMP thread per MPI process -80: -80: Using 1 OpenMP thread per MPI process -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: -80: Dynamic load balancing report: -80: DLB was off during the run due to low measured imbalance. -80: Average load imbalance: 0.2%. -80: The balanceable part of the MD step is 8%, load imbalance is computed from this. -80: Part of the total run time spent waiting due to load imbalance: 0.0%. -80: -80: -80: -80: Dynamic load balancing report: -80: DLB was off during the run due to low measured imbalance. -80: Average load imbalance: 1.7%. -80: The balanceable part of the MD step is 8%, load imbalance is computed from this. -80: Part of the total run time spent waiting due to load imbalance: 0.1%. -80: -80: -80: NOTE: 46 % of the run time was spent communicating energies, -80: you might want to increase some nst* mdp options -80: -80: NOTE: 46 % of the run time was spent communicating energies, -80: you might want to increase some nst* mdp options -80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (12 ms) -80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: Setting the LD random seed to -1754008130 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: The Berendsen barostat does not generate any strictly correct ensemble, -80: and should not be used for new production simulations (in our opinion). -80: We recommend using the C-rescale barostat instead. -80: -80: Generating 1-4 interactions: fudge = 0.5 -80: Setting the LD random seed to -1073909761 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -411582465 -80: -80: Velocities were taken from a Maxwell distribution at 298 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Setting gen_seed to -10020290 -80: -80: -80: Velocities were taken from a Maxwell distribution at 278 K -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: There was 1 WARNING -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: This is simulation 1 out of 2 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 2 MPI processes -80: This is simulation 0 out of 2 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 2 MPI processes -80: Using 1 OpenMP thread per MPI processUsing 1 OpenMP thread per MPI process -80: -80: -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: starting mdrun 'spc2' -80: 2 steps, 0.0 ps. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: -80: Dynamic load balancing report: -80: DLB was off during the run due to low measured imbalance. -80: Average load imbalance: 12.4%. -80: The balanceable part of the MD step is 7%, load imbalance is computed from this. -80: Part of the total run time spent waiting due to load imbalance: 0.9%. -80: -80: -80: -80: Dynamic load balancing report: -80: DLB was off during the run due to low measured imbalance. -80: Average load imbalance: 2.9%. -80: The balanceable part of the MD step is 8%, load imbalance is computed from this. -80: Part of the total run time spent waiting due to load imbalance: 0.2%. -80: -80: -80: NOTE: 46 % of the run time was spent communicating energies, -80: you might want to increase some nst* mdp options -80: -80: NOTE: 46 % of the run time was spent communicating energies, -80: you might want to increase some nst* mdp options -80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (12 ms) -80: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (62 ms total) -80: -80: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest -80: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: Setting the LD random seed to -1343652003 -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to 1475335991 -80: -80: Velocities were taken from a Maxwell distribution at 268 K -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: -80: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You have set rlist larger than the interaction cut-off, but you also have -80: verlet-buffer-tolerance > 0. Will set rlist using -80: verlet-buffer-tolerance. -80: -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: Setting the LD random seed to 1834839419 -80: Setting the LD random seed to -34734353 -80: Setting the LD random seed to 2071971267 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: Generating 1-4 interactions: fudge = 0.5 -80: Generating 1-4 interactions: fudge = 0.5 -80: Generating 1-4 interactions: fudge = 0.5 -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Generated 3 of the 3 non-bonded parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Generated 3 of the 3 1-4 parameter combinations -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Excluding 2 bonded neighbours molecule type 'SOL' -80: -80: Setting gen_seed to -1342190081 -80: -80: -80: Setting gen_seed to -37896194 -80: -80: Velocities were taken from a Maxwell distribution at 278 K -80: -80: Setting gen_seed to -1109950489 -80: -80: Velocities were taken from a Maxwell distribution at 298 K -80: Velocities were taken from a Maxwell distribution at 288 K -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: Number of degrees of freedom in T-Coupling group System is 9.00 -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -80: -80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: Note that mdrun will redetermine rlist based on the actual pair-list setup -80: -80: This run will generate roughly 0 Mb of data -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: -80: You are using a plain Coulomb cut-off, which might produce artifacts. -80: You might want to consider using PME electrostatics. -80: -80: -80: -80: There were 2 NOTEs -80: -80: This run will generate roughly 0 Mb of data -80: -80: This run will generate roughly 0 Mb of data -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -80: -80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -80: -80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -80: -80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 -80: -80: This is simulation 3 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 0 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 2 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: This is simulation 1 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 100 steps, 0.1 ps. -80: starting mdrun 'spc2' -80: 100 steps, 0.1 ps. -80: starting mdrun 'spc2' -80: 100 steps, 0.1 ps. -80: starting mdrun 'spc2' -80: 100 steps, 0.1 ps. -80: -80: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps -80: -80: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps -80: -80: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps -80: -80: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps -80: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 -80: -80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 -80: -80: -80: This is simulation 3 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: -80: This is simulation 2 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: -80: This is simulation 0 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: -80: This is simulation 1 out of 4 running as a composite GROMACS -80: multi-simulation job. Setup for this simulation: -80: -80: Using 1 MPI process -80: Using 1 OpenMP thread -80: -80: Using 1 OpenMP thread -80: -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: -80: NOTE: The number of threads is not equal to the number of (logical) cpus -80: and the -pin option is set to auto: will not pin threads to cpus. -80: This can lead to significant performance degradation. -80: Consider using -pin on (and -pinoffset in case you run multiple jobs). -80: starting mdrun 'spc2' -80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -80: starting mdrun 'spc2' -80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -80: starting mdrun 'spc2' -80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -80: starting mdrun 'spc2' -80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: -80: Writing final coordinates. -80: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (33 ms) -80: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (33 ms total) -80: -80: [----------] Global test environment tear-down -80: [==========] 5 tests from 2 test suites ran. (186 ms total) -80: [ PASSED ] 5 tests. -80/96 Test #80: MdrunMultiSimReplexTests ..................... Passed 0.45 sec -test 81 - Start 81: MdrunMultiSimReplexEquivalenceTests - -81: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" -81: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -81: Test timeout computed to be: 600 -81: [==========] Running 10 tests from 2 test suites. -81: [----------] Global test environment set-up. -81: [----------] 8 tests from LF/ReplicaExchangeTest -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 2 NOTEs -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 268 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 2 NOTEs -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 288 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: This run will generate roughly 0 Mb of data -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 3 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 0 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 2 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 1 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (384 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 268 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: -81: Velocities were taken from a Maxwell distribution at 288 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: -81: This run will generate roughly 0 Mb of data -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 0 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 3 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 1 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 2 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (251 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 268 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: This run will generate roughly 0 Mb of data -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 288 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: This run will generate roughly 0 Mb of data -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: This run will generate roughly 0 Mb of data -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 0 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 1 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 2 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 3 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (248 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 268 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 288 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchaCalculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: ngeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchanReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: geTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 2 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: This is simulation 1 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: This is simulation 3 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: This is simulation 0 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (853 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 0 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: This is simulation 1 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 4.6%. -81: The balanceable part of the MD step is 36%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.6%. -81: -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 3.5%. -81: The balanceable part of the MD step is 48%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.7%. -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (300 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: -81: This run will generate roughly 0 Mb of data -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: There was 1 WARNING -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 1 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: This is simulation 0 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: Using 1 OpenMP thread per MPI process -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 4.7%. -81: The balanceable part of the MD step is 38%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.8%. -81: -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 3.3%. -81: The balanceable part of the MD step is 47%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 1.6%. -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (332 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 3 NOTEs -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExcha -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: ngeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 3 NOTEs -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 0 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: This is simulation 1 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 0.9%. -81: The balanceable part of the MD step is 46%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.4%. -81: -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 0.4%. -81: The balanceable part of the MD step is 46%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.2%. -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (243 ms) -81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -81: 1 -81: -81: -81: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are generating velocities so I am assuming you are equilibrating a -81: system. You are using Parrinello-Rahman pressure coupling, but this can -81: be unstable for equilibration. If your system crashes, try equilibrating -81: first with Berendsen pressure coupling. If you are not equilibrating the -81: system, you can probably ignore this warning. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: -81: This run will generate roughly 0 Mb of data -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 3 NOTEs -81: -81: There was 1 WARNING -81: -81: This run will generate roughly 0 Mb of data -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 1 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI processThis is simulation 0 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 1.3%. -81: The balanceable part of the MD step is 20%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.3%. -81: -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 4.5%. -81: The balanceable part of the MD step is 18%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.8%. -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (236 ms) -81: [----------] 8 tests from LF/ReplicaExchangeTest (2856 ms total) -81: -81: [----------] 2 tests from VV/ReplicaExchangeTest -81: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 268 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 2 NOTEs -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: This run will generate roughly 0 Mb of data -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 288 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 2 NOTEs -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 3 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 1 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 2 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: This is simulation 0 out of 4 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 1 MPI process -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: Using 1 OpenMP thread -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (278 ms) -81: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: -81: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: -81: You have set rlist larger than the interaction cut-off, but you also have -81: verlet-buffer-tolerance > 0. Will set rlist using -81: verlet-buffer-tolerance. -81: -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: Generated 330891 of the 330891 non-bonded parameter combinations -81: Generating 1-4 interactions: fudge = 0.5 -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 298 K -81: -81: Generated 330891 of the 330891 1-4 parameter combinations -81: -81: Excluding 2 bonded neighbours molecule type 'SOL' -81: -81: Velocities were taken from a Maxwell distribution at 278 K -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: There were 2 NOTEs -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: This run will generate roughly 0 Mb of data -81: Number of degrees of freedom in T-Coupling group System is 27.00 -81: -81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -81: -81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm -81: -81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm -81: -81: Note that mdrun will redetermine rlist based on the actual pair-list setup -81: -81: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: -81: You are using a plain Coulomb cut-off, which might produce artifacts. -81: You might want to consider using PME electrostatics. -81: -81: -81: -81: This run will generate roughly 0 Mb of data -81: -81: There were 2 NOTEs -81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 -81: -81: This is simulation 1 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: This is simulation 0 out of 2 running as a composite GROMACS -81: multi-simulation job. Setup for this simulation: -81: -81: Using 2 MPI processes -81: Using 1 OpenMP thread per MPI process -81: -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: -81: NOTE: The number of threads is not equal to the number of (logical) cpus -81: and the -pin option is set to auto: will not pin threads to cpus. -81: This can lead to significant performance degradation. -81: Consider using -pin on (and -pinoffset in case you run multiple jobs). -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: starting mdrun 'spc2' -81: 16 steps, 0.0 ps. -81: -81: Writing final coordinates. -81: -81: Writing final coordinates. -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 1.5%. -81: The balanceable part of the MD step is 33%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.5%. -81: -81: -81: -81: Dynamic load balancing report: -81: DLB was off during the run due to low measured imbalance. -81: Average load imbalance: 2.1%. -81: The balanceable part of the MD step is 33%, load imbalance is computed from this. -81: Part of the total run time spent waiting due to load imbalance: 0.7%. -81: -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file -81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -81: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (239 ms) -81: [----------] 2 tests from VV/ReplicaExchangeTest (518 ms total) -81: -81: [----------] Global test environment tear-down -81: [==========] 10 tests from 2 test suites ran. (3462 ms total) -81: [ PASSED ] 10 tests. -81/96 Test #81: MdrunMultiSimReplexEquivalenceTests .......... Passed 3.75 sec -test 82 - Start 82: MdrunMpi1RankPmeTests - -82: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" -82: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -82: Test timeout computed to be: 600 -82: [==========] Running 19 tests from 1 test suite. -82: [----------] Global test environment set-up. -82: [----------] 19 tests from ReproducesEnergies/PmeTest -82: Setting the LD random seed to -68097 -82: -82: Generated 8 of the 10 non-bonded parameter combinations -82: -82: Excluding 2 bonded neighbours molecule type 'Methanol' -82: -82: Excluding 2 bonded neighbours molecule type 'SOL' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -82: Number of degrees of freedom in T-Coupling group rest is 12.00 -82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -82: NVE simulation: will use the initial temperature of 1046.791 K for -82: determining the Verlet buffer size -82: -82: -82: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -82: -82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -82: -82: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: Calculating fourier grid dimensions for X Y Z -82: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -82: -82: Estimate for the relative computational load of the PME mesh part: 1.00 -82: -82: This run will generate roughly 0 Mb of data -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -82: The optimal PME mesh load for parallel simulations is below 0.5 -82: and for highly parallel simulations between 0.25 and 0.33, -82: for higher performance, increase the cut-off and the PME grid spacing. -82: -82: -82: -82: There were 2 NOTEs -82: -82: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -82: For a correct single-point energy evaluation with nsteps = 0, use -82: continuation = yes to avoid constraining the input coordinates. -82: -82: Setting the LD random seed to 1593425917 -82: -82: Generated 8 of the 10 non-bonded parameter combinations -82: -82: Excluding 2 bonded neighbours molecule type 'Methanol' -82: -82: Excluding 2 bonded neighbours molecule type 'SOL' -82: -82: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -82: -82: Searching the wall atom type(s) -82: Number of degrees of freedom in T-Coupling group rest is 13.00 -82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -82: -82: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -82: NVE simulation: will use the initial temperature of 966.268 K for -82: determining the Verlet buffer size -82: -82: -82: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -82: -82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -82: -82: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -82: -82: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -82: -82: Note that mdrun will redetermine rlist based on the actual pair-list setup -82: Calculating fourier grid dimensions for X Y Z -82: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 -82: -82: Estimate for the relative computational load of the PME mesh part: 1.00 -82: -82: This run will generate roughly 0 Mb of data -82: -82: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -82: The optimal PME mesh load for parallel simulations is below 0.5 -82: and for highly parallel simulations between 0.25 and 0.33, -82: for higher performance, increase the cut-off and the PME grid spacing. -82: -82: -82: -82: There were 3 NOTEs -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI process -82: Using 2 OpenMP threads -82: -82: -82: NOTE: The number of threads is not equal to the number of (logical) cpus -82: and the -pin option is set to auto: will not pin threads to cpus. -82: This can lead to significant performance degradation. -82: Consider using -pin on (and -pinoffset in case you run multiple jobs). -82: starting mdrun 'spc-and-methanol' -82: 20 steps, 0.0 ps. -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.027 0.014 199.0 -82: (ns/day) (hour/ns) -82: Performance: 132.653 0.181 -82: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (160 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI process -82: Using 2 OpenMP threads -82: -82: -82: NOTE: The number of threads is not equal to the number of (logical) cpus -82: and the -pin option is set to auto: will not pin threads to cpus. -82: This can lead to significant performance degradation. -82: Consider using -pin on (and -pinoffset in case you run multiple jobs). -82: starting mdrun 'spc-and-methanol' -82: 20 steps, 0.0 ps. -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.024 0.012 199.3 -82: (ns/day) (hour/ns) -82: Performance: 152.212 0.158 -82: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (17 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI process -82: Using 2 OpenMP threads -82: -82: -82: NOTE: The number of threads is not equal to the number of (logical) cpus -82: and the -pin option is set to auto: will not pin threads to cpus. -82: This can lead to significant performance degradation. -82: Consider using -pin on (and -pinoffset in case you run multiple jobs). -82: starting mdrun 'spc-and-methanol' -82: 0 steps, 0.0 ps. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.004 0.002 194.9 -82: (ns/day) (hour/ns) -82: Performance: 42.983 0.558 -82: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (511 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets using PME rank(s) but the simulation is using only one rank -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -82: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -82: Can not increase nstlist because an NVE ensemble is used -82: Using 1 MPI process -82: Using 2 OpenMP threads -82: -82: -82: NOTE: The number of threads is not equal to the number of (logical) cpus -82: and the -pin option is set to auto: will not pin threads to cpus. -82: This can lead to significant performance degradation. -82: Consider using -pin on (and -pinoffset in case you run multiple jobs). -82: starting mdrun 'spc-and-methanol' -82: 20 steps, 0.0 ps. -82: -82: Writing final coordinates. -82: -82: Core t (s) Wall t (s) (%) -82: Time: 0.030 0.015 199.5 -82: (ns/day) (hour/ns) -82: Performance: 121.242 0.198 -82: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file -82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (20 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped -82: Test is being skipped because: -82: it targets GPU execution, but no compatible devices were detected -82: PME GPU does not support: -82: Non-GPU build of GROMACS. -82: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -82: [----------] 19 tests from ReproducesEnergies/PmeTest (712 ms total) -82: -82: [----------] Global test environment tear-down -82: [==========] 19 tests from 1 test suite ran. (753 ms total) -82: [ PASSED ] 4 tests. -82: [ SKIPPED ] 15 tests, listed below: -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -82/96 Test #82: MdrunMpi1RankPmeTests ........................ Passed 1.03 sec -test 83 - Start 83: MdrunMpi2RankPmeTests - -83: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" -83: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -83: Test timeout computed to be: 600 -83: [==========] Running 19 tests from 1 test suite. -83: [----------] Global test environment set-up. -83: [----------] 19 tests from ReproducesEnergies/PmeTest -83: Setting the LD random seed to -33759233 -83: -83: Generated 8 of the 10 non-bonded parameter combinations -83: -83: Excluding 2 bonded neighbours molecule type 'Methanol' -83: -83: Excluding 2 bonded neighbours molecule type 'SOL' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -83: Number of degrees of freedom in T-Coupling group rest is 12.00 -83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -83: -83: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -83: -83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -83: NVE simulation: will use the initial temperature of 1046.791 K for -83: determining the Verlet buffer size -83: -83: -83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: Calculating fourier grid dimensions for X Y Z -83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -83: -83: Estimate for the relative computational load of the PME mesh part: 1.00 -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -83: The optimal PME mesh load for parallel simulations is below 0.5 -83: and for highly parallel simulations between 0.25 and 0.33, -83: for higher performance, increase the cut-off and the PME grid spacing. -83: -83: -83: -83: This run will generate roughly 0 Mb of data -83: -83: There were 2 NOTEs -83: -83: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -83: For a correct single-point energy evaluation with nsteps = 0, use -83: continuation = yes to avoid constraining the input coordinates. -83: -83: Setting the LD random seed to 1106558702 -83: -83: Generated 8 of the 10 non-bonded parameter combinations -83: -83: Excluding 2 bonded neighbours molecule type 'Methanol' -83: -83: Excluding 2 bonded neighbours molecule type 'SOL' -83: -83: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc-and-methanol.gro' -83: -83: Searching the wall atom type(s) -83: Number of degrees of freedom in T-Coupling group rest is 13.00 -83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -83: -83: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -83: NVE simulation: will use the initial temperature of 966.268 K for -83: determining the Verlet buffer size -83: -83: -83: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 -83: -83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K -83: -83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -83: -83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -83: -83: Note that mdrun will redetermine rlist based on the actual pair-list setup -83: Calculating fourier grid dimensions for X Y Z -83: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 -83: -83: Estimate for the relative computational load of the PME mesh part: 1.00 -83: -83: This run will generate roughly 0 Mb of data -83: -83: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: -83: The optimal PME mesh load for parallel simulations is below 0.5 -83: and for highly parallel simulations between 0.25 and 0.33, -83: for higher performance, increase the cut-off and the PME grid spacing. -83: -83: -83: -83: There were 3 NOTEs -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 20 steps, 0.0 ps. -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.4%. -83: The balanceable part of the MD step is 10%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.1%. -83: -83: -83: NOTE: 24 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.064 0.016 398.4 -83: (ns/day) (hour/ns) -83: Performance: 113.715 0.211 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (166 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 20 steps, 0.0 ps. -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 2.7%. -83: The balanceable part of the MD step is 10%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.3%. -83: -83: -83: NOTE: 18 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.051 0.013 398.1 -83: (ns/day) (hour/ns) -83: Performance: 141.228 0.170 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (18 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 0 steps, 0.0 ps. -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.006 0.002 381.9 -83: (ns/day) (hour/ns) -83: Performance: 51.388 0.467 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (496 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 20 steps, 0.0 ps. -83: -83: Writing final coordinates. -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.063 0.016 397.5 -83: (ns/day) (hour/ns) -83: Performance: 114.511 0.210 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (93 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 20 steps, 0.0 ps. -83: -83: Writing final coordinates. -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.057 0.014 396.5 -83: (ns/day) (hour/ns) -83: Performance: 126.038 0.190 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (20 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 0 steps, 0.0 ps. -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.009 0.002 355.9 -83: (ns/day) (hour/ns) -83: Performance: 35.493 0.676 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (326 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu -83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -83: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -83: Can not increase nstlist because an NVE ensemble is used -83: Using 2 MPI processes -83: Using 2 OpenMP threads per MPI process -83: -83: -83: NOTE: The number of threads is not equal to the number of (logical) cpus -83: and the -pin option is set to auto: will not pin threads to cpus. -83: This can lead to significant performance degradation. -83: Consider using -pin on (and -pinoffset in case you run multiple jobs). -83: starting mdrun 'spc-and-methanol' -83: 20 steps, 0.0 ps. -83: -83: Writing final coordinates. -83: -83: -83: Dynamic load balancing report: -83: DLB was off during the run due to low measured imbalance. -83: Average load imbalance: 1.3%. -83: The balanceable part of the MD step is 9%, load imbalance is computed from this. -83: Part of the total run time spent waiting due to load imbalance: 0.1%. -83: -83: -83: NOTE: 20 % of the run time was spent communicating energies, -83: you might want to increase some nst* mdp options -83: -83: Core t (s) Wall t (s) (%) -83: Time: 0.054 0.014 397.2 -83: (ns/day) (hour/ns) -83: Performance: 133.905 0.179 -83: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file -83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (20 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) -83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) -83: [----------] 19 tests from ReproducesEnergies/PmeTest (1143 ms total) -83: -83: [----------] Global test environment tear-down -83: [==========] 19 tests from 1 test suite ran. (1178 ms total) -83: [ PASSED ] 7 tests. -83: [ SKIPPED ] 12 tests, listed below: -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu -83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu -83/96 Test #83: MdrunMpi2RankPmeTests ........................ Passed 1.45 sec -test 84 - Start 84: MdrunCoordinationBasicTests1Rank - -84: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" -84: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -84: Test timeout computed to be: 1920 -84: [==========] Running 1 test from 1 test suite. -84: [----------] Global test environment set-up. -84: [----------] 1 test from BasicPropagators/PeriodicActionsTest -84: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.008 0.008 99.6 -84: (ns/day) (hour/ns) -84: Performance: 188.472 0.127 -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (1) -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: There were 3 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 292.318 0.082 -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: Setting nstcalcenergy (100) equal to nstenergy (4) -84: -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (1). -84: Other settings require a global communication frequency of 4. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 4. -84: -84: -84: There were 5 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.004 0.004 99.4 -84: (ns/day) (hour/ns) -84: Performance: 341.137 0.070 -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (1). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.005 0.005 99.5 -84: (ns/day) (hour/ns) -84: Performance: 281.164 0.085 -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (1). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.007 0.007 99.6 -84: (ns/day) (hour/ns) -84: Performance: 203.616 0.118 -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: -84: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -84: that with the Verlet scheme, nstlist has no effect on the accuracy of -84: your simulation. -84: -84: -84: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -84: setting nstcomm equal to nstcalcenergy for less overhead -84: -84: Generated 1 of the 1 non-bonded parameter combinations -84: -84: Excluding 1 bonded neighbours molecule type 'Argon' -84: -84: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -84: Number of degrees of freedom in T-Coupling group System is 33.00 -84: -84: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: NVE simulation: will use the initial temperature of 68.810 K for -84: determining the Verlet buffer size -84: -84: -84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -84: -84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -84: -84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -84: -84: Note that mdrun will redetermine rlist based on the actual pair-list setup -84: -84: This run will generate roughly 0 Mb of data -84: -84: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -84: COM removal frequency is set to (1). -84: Other settings require a global communication frequency of 100. -84: Note that this will require additional global communication steps, -84: which will reduce performance when using multiple ranks. -84: Consider setting nstcomm to a multiple of 100. -84: -84: -84: There were 4 NOTEs -84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -84: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -84: Can not increase nstlist because an NVE ensemble is used -84: Using 1 MPI process -84: Using 1 OpenMP thread -84: -84: -84: NOTE: Thread affinity was not set. -84: starting mdrun 'Argon' -84: 16 steps, 0.0 ps. -84: -84: Writing final coordinates. -84: -84: Core t (s) Wall t (s) (%) -84: Time: 0.009 0.009 99.7 -84: (ns/day) (hour/ns) -84: Performance: 162.215 0.148 -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -84: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -84: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (68 ms) -84: [----------] 1 test from BasicPropagators/PeriodicActionsTest (68 ms total) -84: -84: [----------] Global test environment tear-down -84: [==========] 1 test from 1 test suite ran. (88 ms total) -84: [ PASSED ] 1 test. -84/96 Test #84: MdrunCoordinationBasicTests1Rank ............. Passed 0.36 sec -test 85 - Start 85: MdrunCoordinationBasicTests2Ranks - -85: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" -85: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -85: Test timeout computed to be: 1920 -85: [==========] Running 1 test from 1 test suite. -85: [----------] Global test environment set-up. -85: [----------] 1 test from BasicPropagators/PeriodicActionsTest -85: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.1%. -85: The balanceable part of the MD step is 55%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.1%. -85: -85: -85: NOTE: 49 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.097 0.049 199.7 -85: (ns/day) (hour/ns) -85: Performance: 30.169 0.796 -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (1) -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: There were 3 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.2%. -85: The balanceable part of the MD step is 55%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.1%. -85: -85: -85: NOTE: 43 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.1 -85: (ns/day) (hour/ns) -85: Performance: 236.255 0.102 -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: Setting nstcalcenergy (100) equal to nstenergy (4) -85: -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (1). -85: Other settings require a global communication frequency of 4. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 4. -85: -85: -85: There were 5 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.5%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.2%. -85: -85: -85: NOTE: 44 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.012 0.006 198.1 -85: (ns/day) (hour/ns) -85: Performance: 238.959 0.100 -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (1). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.6%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.3%. -85: -85: -85: NOTE: 47 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.020 0.010 198.8 -85: (ns/day) (hour/ns) -85: Performance: 144.542 0.166 -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (1). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.6%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.3%. -85: -85: -85: NOTE: 46 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.017 0.009 198.6 -85: (ns/day) (hour/ns) -85: Performance: 168.999 0.142 -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: -85: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -85: that with the Verlet scheme, nstlist has no effect on the accuracy of -85: your simulation. -85: -85: -85: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -85: setting nstcomm equal to nstcalcenergy for less overhead -85: -85: Generated 1 of the 1 non-bonded parameter combinations -85: -85: Excluding 1 bonded neighbours molecule type 'Argon' -85: -85: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -85: Number of degrees of freedom in T-Coupling group System is 33.00 -85: -85: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: NVE simulation: will use the initial temperature of 68.810 K for -85: determining the Verlet buffer size -85: -85: -85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -85: -85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -85: -85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -85: -85: Note that mdrun will redetermine rlist based on the actual pair-list setup -85: -85: This run will generate roughly 0 Mb of data -85: -85: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -85: COM removal frequency is set to (1). -85: Other settings require a global communication frequency of 100. -85: Note that this will require additional global communication steps, -85: which will reduce performance when using multiple ranks. -85: Consider setting nstcomm to a multiple of 100. -85: -85: -85: There were 4 NOTEs -85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -85: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -85: Can not increase nstlist because an NVE ensemble is used -85: Using 2 MPI processes -85: Using 1 OpenMP thread per MPI process -85: -85: -85: NOTE: The number of threads is not equal to the number of (logical) cpus -85: and the -pin option is set to auto: will not pin threads to cpus. -85: This can lead to significant performance degradation. -85: Consider using -pin on (and -pinoffset in case you run multiple jobs). -85: starting mdrun 'Argon' -85: 16 steps, 0.0 ps. -85: -85: Writing final coordinates. -85: -85: -85: Dynamic load balancing report: -85: DLB was off during the run due to low measured imbalance. -85: Average load imbalance: 0.6%. -85: The balanceable part of the MD step is 51%, load imbalance is computed from this. -85: Part of the total run time spent waiting due to load imbalance: 0.3%. -85: -85: -85: NOTE: 45 % of the run time was spent communicating energies, -85: you might want to increase some nst* mdp options -85: -85: Core t (s) Wall t (s) (%) -85: Time: 0.013 0.007 198.2 -85: (ns/day) (hour/ns) -85: Performance: 218.248 0.110 -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -85: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -85: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (133 ms) -85: [----------] 1 test from BasicPropagators/PeriodicActionsTest (133 ms total) -85: -85: [----------] Global test environment tear-down -85: [==========] 1 test from 1 test suite ran. (168 ms total) -85: [ PASSED ] 1 test. -85/96 Test #85: MdrunCoordinationBasicTests2Ranks ............ Passed 0.44 sec -test 86 - Start 86: MdrunCoordinationCouplingTests1Rank - -86: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" -86: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -86: Test timeout computed to be: 1920 -86: [==========] Running 25 tests from 1 test suite. -86: [----------] Global test environment set-up. -86: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 156.834 0.153 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.4 -86: (ns/day) (hour/ns) -86: Performance: 305.434 0.079 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.5 -86: (ns/day) (hour/ns) -86: Performance: 304.874 0.079 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 214.797 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 221.804 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.8 -86: (ns/day) (hour/ns) -86: Performance: 94.787 0.253 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (78 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 197.626 0.121 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.6 -86: (ns/day) (hour/ns) -86: Performance: 227.412 0.106 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.4 -86: (ns/day) (hour/ns) -86: Performance: 244.361 0.098 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 169.961 0.141 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 253.033 0.095 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.016 0.016 99.8 -86: (ns/day) (hour/ns) -86: Performance: 92.193 0.260 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (78 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 236.011 0.102 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: -86: There were 3 NOTEs -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.4 -86: (ns/day) (hour/ns) -86: Performance: 274.573 0.087 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 165.643 0.145 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 165.243 0.145 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 205.005 0.117 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.4 -86: (ns/day) (hour/ns) -86: Performance: 187.817 0.128 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (75 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.4 -86: (ns/day) (hour/ns) -86: Performance: 185.666 0.129 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.1 -86: (ns/day) (hour/ns) -86: Performance: 283.650 0.085 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 232.002 0.103 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 153.547 0.156 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 175.186 0.137 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 238.922 0.100 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (76 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 219.137 0.110 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 2 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 262.936 0.091 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.4 -86: (ns/day) (hour/ns) -86: Performance: 314.975 0.076 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.4 -86: (ns/day) (hour/ns) -86: Performance: 235.758 0.102 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 182.780 0.131 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 219.504 0.109 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (67 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 213.287 0.113 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 207.079 0.116 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 99.3 -86: (ns/day) (hour/ns) -86: Performance: 352.719 0.068 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.6 -86: (ns/day) (hour/ns) -86: Performance: 161.509 0.149 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 198.434 0.121 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 147.517 0.163 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (72 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 188.173 0.128 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 231.558 0.104 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 98.5 -86: (ns/day) (hour/ns) -86: Performance: 353.529 0.068 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 212.412 0.113 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 216.040 0.111 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: There were 2 NOTEs -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.7 -86: (ns/day) (hour/ns) -86: Performance: 138.984 0.173 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (73 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 213.947 0.112 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 99.3 -86: (ns/day) (hour/ns) -86: Performance: 347.271 0.069 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: There were 2 NOTEs -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 169.648 0.141 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 244.798 0.098 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.4 -86: (ns/day) (hour/ns) -86: Performance: 190.825 0.126 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: There were 2 NOTEs -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 168.696 0.142 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (72 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.111 0.111 99.9 -86: (ns/day) (hour/ns) -86: Performance: 13.212 1.817 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 98.8 -86: (ns/day) (hour/ns) -86: Performance: 276.918 0.087 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 244.478 0.098 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 219.645 0.109 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 208.940 0.115 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.7 -86: (ns/day) (hour/ns) -86: Performance: 155.779 0.154 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (182 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 174.269 0.138 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 222.043 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.2 -86: (ns/day) (hour/ns) -86: Performance: 253.637 0.095 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.4 -86: (ns/day) (hour/ns) -86: Performance: 176.511 0.136 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.2 -86: (ns/day) (hour/ns) -86: Performance: 200.821 0.120 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 199.101 0.121 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (76 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 3 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.4 -86: (ns/day) (hour/ns) -86: Performance: 165.790 0.145 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: There were 3 NOTEs -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.1 -86: (ns/day) (hour/ns) -86: Performance: 295.969 0.081 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 221.883 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.1 -86: (ns/day) (hour/ns) -86: Performance: 268.611 0.089 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.1 -86: (ns/day) (hour/ns) -86: Performance: 209.837 0.114 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 204.576 0.117 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (75 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 214.625 0.112 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 98.9 -86: (ns/day) (hour/ns) -86: Performance: 331.929 0.072 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 256.339 0.094 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 216.305 0.111 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: -86: There were 3 NOTEs -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.3 -86: (ns/day) (hour/ns) -86: Performance: 201.927 0.119 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -86: 1 -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 165.505 0.145 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (75 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 220.273 0.109 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 2 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 188.761 0.127 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 3 NOTEs -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.4 -86: (ns/day) (hour/ns) -86: Performance: 238.561 0.101 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.4 -86: (ns/day) (hour/ns) -86: Performance: 239.712 0.100 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 180.668 0.133 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.6 -86: (ns/day) (hour/ns) -86: Performance: 142.326 0.169 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (79 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 241.876 0.099 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.024 0.024 99.8 -86: (ns/day) (hour/ns) -86: Performance: 59.986 0.400 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 265.772 0.090 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.3 -86: (ns/day) (hour/ns) -86: Performance: 241.440 0.099 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 181.413 0.132 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.012 0.012 99.7 -86: (ns/day) (hour/ns) -86: Performance: 124.787 0.192 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (96 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.6 -86: (ns/day) (hour/ns) -86: Performance: 236.591 0.101 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.004 0.004 99.4 -86: (ns/day) (hour/ns) -86: Performance: 354.465 0.068 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.6 -86: (ns/day) (hour/ns) -86: Performance: 248.171 0.097 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 221.524 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 2 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 212.193 0.113 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 243.579 0.099 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (74 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.7 -86: (ns/day) (hour/ns) -86: Performance: 173.900 0.138 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 262.667 0.091 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: There were 2 NOTEs -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.005 0.005 99.5 -86: (ns/day) (hour/ns) -86: Performance: 289.938 0.083 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.6 -86: (ns/day) (hour/ns) -86: Performance: 226.609 0.106 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 222.661 0.108 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.6 -86: (ns/day) (hour/ns) -86: Performance: 224.405 0.107 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (70 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.7 -86: (ns/day) (hour/ns) -86: Performance: 216.549 0.111 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: -86: There were 3 NOTEs -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.7 -86: (ns/day) (hour/ns) -86: Performance: 247.811 0.097 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 4. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 4. -86: -86: -86: There were 4 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.7 -86: (ns/day) (hour/ns) -86: Performance: 239.927 0.100 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.8 -86: (ns/day) (hour/ns) -86: Performance: 208.213 0.115 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.8 -86: (ns/day) (hour/ns) -86: Performance: 168.881 0.142 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 100. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 100. -86: -86: -86: There were 4 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.8 -86: (ns/day) (hour/ns) -86: Performance: 161.955 0.148 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (74 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.8 -86: (ns/day) (hour/ns) -86: Performance: 188.825 0.127 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.7 -86: (ns/day) (hour/ns) -86: Performance: 216.093 0.111 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.8 -86: (ns/day) (hour/ns) -86: Performance: 186.385 0.129 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.8 -86: (ns/day) (hour/ns) -86: Performance: 138.130 0.174 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.8 -86: (ns/day) (hour/ns) -86: Performance: 136.686 0.176 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.8 -86: (ns/day) (hour/ns) -86: Performance: 142.234 0.169 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (81 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.9 -86: (ns/day) (hour/ns) -86: Performance: 98.044 0.245 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.8 -86: (ns/day) (hour/ns) -86: Performance: 162.785 0.147 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.8 -86: (ns/day) (hour/ns) -86: Performance: 172.982 0.139 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.8 -86: (ns/day) (hour/ns) -86: Performance: 174.556 0.137 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.014 0.014 99.7 -86: (ns/day) (hour/ns) -86: Performance: 105.333 0.228 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -86: NVE simulation: will use the initial temperature of 68.810 K for -86: determining the Verlet buffer size -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Can not increase nstlist because an NVE ensemble is used -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.8 -86: (ns/day) (hour/ns) -86: Performance: 100.447 0.239 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (104 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 151.645 0.158 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 243.089 0.099 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 246.246 0.097 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.066 0.066 99.9 -86: (ns/day) (hour/ns) -86: Performance: 22.342 1.074 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.018 0.018 99.8 -86: (ns/day) (hour/ns) -86: Performance: 81.404 0.295 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.027 0.027 99.9 -86: (ns/day) (hour/ns) -86: Performance: 54.952 0.437 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (179 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.018 0.018 99.8 -86: (ns/day) (hour/ns) -86: Performance: 83.020 0.289 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.014 0.014 99.8 -86: (ns/day) (hour/ns) -86: Performance: 102.968 0.233 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.036 0.036 99.9 -86: (ns/day) (hour/ns) -86: Performance: 40.490 0.593 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.039 0.039 99.7 -86: (ns/day) (hour/ns) -86: Performance: 37.798 0.635 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.8 -86: (ns/day) (hour/ns) -86: Performance: 98.279 0.244 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: -86: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -86: The Berendsen barostat does not generate any strictly correct ensemble, -86: and should not be used for new production simulations (in our opinion). -86: We recommend using the C-rescale barostat instead. -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: There was 1 WARNING -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.017 0.017 99.8 -86: (ns/day) (hour/ns) -86: Performance: 85.023 0.282 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (180 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 176.526 0.136 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.3 -86: (ns/day) (hour/ns) -86: Performance: 188.346 0.127 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 197.956 0.121 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: There were 2 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.016 0.016 99.8 -86: (ns/day) (hour/ns) -86: Performance: 93.711 0.256 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.6 -86: (ns/day) (hour/ns) -86: Performance: 151.448 0.158 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 141.366 0.170 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (95 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: -86: There were 2 NOTEs -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.6 -86: (ns/day) (hour/ns) -86: Performance: 165.474 0.145 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 213.650 0.112 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.4 -86: (ns/day) (hour/ns) -86: Performance: 217.997 0.110 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.6 -86: (ns/day) (hour/ns) -86: Performance: 172.890 0.139 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.028 0.028 99.9 -86: (ns/day) (hour/ns) -86: Performance: 52.381 0.458 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 3 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.6 -86: (ns/day) (hour/ns) -86: Performance: 169.071 0.142 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (104 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.6 -86: (ns/day) (hour/ns) -86: Performance: 146.409 0.164 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 4 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.1 -86: (ns/day) (hour/ns) -86: Performance: 212.706 0.113 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 180.848 0.133 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 165.719 0.145 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 5 NOTEs -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.6 -86: (ns/day) (hour/ns) -86: Performance: 99.086 0.242 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: MTTK coupling is deprecated and will soon be removed -86: -86: -86: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: for current Trotter decomposition methods with vv, nsttcouple and -86: nstpcouple must be equal. Both have been reset to -86: min(nsttcouple,nstpcouple) = 2 -86: -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -86: COM removal frequency is set to (5). -86: Other settings require a global communication frequency of 2. -86: Note that this will require additional global communication steps, -86: which will reduce performance when using multiple ranks. -86: Consider setting nstcomm to a multiple of 2. -86: -86: -86: There were 5 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.009 0.009 99.5 -86: (ns/day) (hour/ns) -86: Performance: 169.798 0.141 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (90 ms) -86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: There were 2 NOTEs -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.010 0.010 99.7 -86: (ns/day) (hour/ns) -86: Performance: 146.919 0.163 -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (1) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.008 0.008 99.5 -86: (ns/day) (hour/ns) -86: Performance: 193.413 0.124 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: Setting nstcalcenergy (100) equal to nstenergy (4) -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.006 0.006 99.5 -86: (ns/day) (hour/ns) -86: Performance: 240.592 0.100 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.007 0.007 99.5 -86: (ns/day) (hour/ns) -86: Performance: 206.683 0.116 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: -86: There were 2 NOTEs -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.011 0.011 99.6 -86: (ns/day) (hour/ns) -86: Performance: 136.074 0.176 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -86: -86: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -86: that with the Verlet scheme, nstlist has no effect on the accuracy of -86: your simulation. -86: -86: -86: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -86: setting nstcomm equal to nstcalcenergy for less overhead -86: -86: Generated 1 of the 1 non-bonded parameter combinations -86: -86: Excluding 1 bonded neighbours molecule type 'Argon' -86: -86: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -86: Number of degrees of freedom in T-Coupling group System is 33.00 -86: -86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -86: -86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -86: -86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -86: -86: Note that mdrun will redetermine rlist based on the actual pair-list setup -86: -86: This run will generate roughly 0 Mb of data -86: -86: There were 2 NOTEs -86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -86: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -86: -86: Using 1 MPI process -86: Using 1 OpenMP thread -86: -86: -86: NOTE: Thread affinity was not set. -86: starting mdrun 'Argon' -86: 16 steps, 0.0 ps. -86: -86: Writing final coordinates. -86: -86: Core t (s) Wall t (s) (%) -86: Time: 0.015 0.015 99.9 -86: (ns/day) (hour/ns) -86: Performance: 96.962 0.248 -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -86: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (86 ms) -86: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (2327 ms total) -86: -86: [----------] Global test environment tear-down -86: [==========] 25 tests from 1 test suite ran. (2351 ms total) -86: [ PASSED ] 25 tests. -86/96 Test #86: MdrunCoordinationCouplingTests1Rank .......... Passed 2.62 sec -test 87 - Start 87: MdrunCoordinationCouplingTests2Ranks - -87: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" -87: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -87: Test timeout computed to be: 1920 -87: [==========] Running 25 tests from 1 test suite. -87: [----------] Global test environment set-up. -87: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 55%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 198.8 -87: (ns/day) (hour/ns) -87: Performance: 139.763 0.172 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 0.4%. -87: The balanceable part of the MD step is 51%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.2%. -87: -87: -87: NOTE: 50 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.955 0.478 200.0 -87: (ns/day) (hour/ns) -87: Performance: 3.076 7.803 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.7%. -87: The balanceable part of the MD step is 0%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.0%. -87: -87: -87: NOTE: 41 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 1.316 0.658 200.0 -87: (ns/day) (hour/ns) -87: Performance: 2.233 10.750 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 2 time 0.008 Last energy frame read 4 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.1%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 50 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.283 0.142 199.9 -87: (ns/day) (hour/ns) -87: Performance: 10.375 2.313 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.6%. -87: The balanceable part of the MD step is 39%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.0%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.3 -87: (ns/day) (hour/ns) -87: Performance: 239.810 0.100 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 36%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.0 -87: (ns/day) (hour/ns) -87: Performance: 238.658 0.101 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1745 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.7%. -87: The balanceable part of the MD step is 52%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.027 0.013 199.3 -87: (ns/day) (hour/ns) -87: Performance: 109.768 0.219 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 4.7%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.2%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.6 -87: (ns/day) (hour/ns) -87: Performance: 201.504 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 4.7%. -87: The balanceable part of the MD step is 43%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.0%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.0 -87: (ns/day) (hour/ns) -87: Performance: 182.536 0.131 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 8.7%. -87: The balanceable part of the MD step is 42%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 3.6%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 199.4 -87: (ns/day) (hour/ns) -87: Performance: 85.164 0.282 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 9.0%. -87: The balanceable part of the MD step is 42%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 3.7%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.026 0.013 199.2 -87: (ns/day) (hour/ns) -87: Performance: 112.760 0.213 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.2%. -87: The balanceable part of the MD step is 43%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.5%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 197.8 -87: (ns/day) (hour/ns) -87: Performance: 189.940 0.126 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (105 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 29%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.4%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.022 0.011 198.1 -87: (ns/day) (hour/ns) -87: Performance: 130.643 0.184 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.8%. -87: The balanceable part of the MD step is 53%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 196.8 -87: (ns/day) (hour/ns) -87: Performance: 235.839 0.102 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.4%. -87: The balanceable part of the MD step is 46%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.1 -87: (ns/day) (hour/ns) -87: Performance: 235.142 0.102 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.6%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.030 0.015 199.2 -87: (ns/day) (hour/ns) -87: Performance: 96.111 0.250 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.6%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.2 -87: (ns/day) (hour/ns) -87: Performance: 224.585 0.107 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.0%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.8 -87: (ns/day) (hour/ns) -87: Performance: 162.482 0.148 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (90 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.5%. -87: The balanceable part of the MD step is 53%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.5 -87: (ns/day) (hour/ns) -87: Performance: 199.899 0.120 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.1%. -87: The balanceable part of the MD step is 49%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 197.7 -87: (ns/day) (hour/ns) -87: Performance: 324.583 0.074 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.6%. -87: The balanceable part of the MD step is 43%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.004 197.7 -87: (ns/day) (hour/ns) -87: Performance: 327.970 0.073 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.9%. -87: The balanceable part of the MD step is 40%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.028 0.014 198.9 -87: (ns/day) (hour/ns) -87: Performance: 105.384 0.228 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 225.481 0.106 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.2%. -87: The balanceable part of the MD step is 41%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.9%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.005 197.0 -87: (ns/day) (hour/ns) -87: Performance: 268.149 0.090 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (77 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.6 -87: (ns/day) (hour/ns) -87: Performance: 191.737 0.125 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 197.5 -87: (ns/day) (hour/ns) -87: Performance: 237.829 0.101 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Last energy frame read 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.1 -87: (ns/day) (hour/ns) -87: Performance: 247.394 0.097 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.6 -87: (ns/day) (hour/ns) -87: Performance: 197.928 0.121 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.7 -87: (ns/day) (hour/ns) -87: Performance: 164.599 0.146 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 197.6 -87: (ns/day) (hour/ns) -87: Performance: 226.926 0.106 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (73 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.2 -87: (ns/day) (hour/ns) -87: Performance: 217.190 0.111 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.5 -87: (ns/day) (hour/ns) -87: Performance: 187.932 0.128 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.5 -87: (ns/day) (hour/ns) -87: Performance: 297.218 0.081 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 1 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.008 198.6 -87: (ns/day) (hour/ns) -87: Performance: 174.967 0.137 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.031 0.015 198.9 -87: (ns/day) (hour/ns) -87: Performance: 95.125 0.252 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.030 0.015 199.2 -87: (ns/day) (hour/ns) -87: Performance: 97.281 0.247 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (90 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.7 -87: (ns/day) (hour/ns) -87: Performance: 157.776 0.152 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.2 -87: (ns/day) (hour/ns) -87: Performance: 222.895 0.108 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.004 196.1 -87: (ns/day) (hour/ns) -87: Performance: 328.775 0.073 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Last energy frame read 4 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 198.6 -87: (ns/day) (hour/ns) -87: Performance: 167.585 0.143 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.6 -87: (ns/day) (hour/ns) -87: Performance: 166.244 0.144 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 212.226 0.113 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (80 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.2 -87: (ns/day) (hour/ns) -87: Performance: 198.048 0.121 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 198.0 -87: (ns/day) (hour/ns) -87: Performance: 294.020 0.082 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 197.3 -87: (ns/day) (hour/ns) -87: Performance: 203.266 0.118 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.041 0.021 199.3 -87: (ns/day) (hour/ns) -87: Performance: 71.177 0.337 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.031 0.016 198.8 -87: (ns/day) (hour/ns) -87: Performance: 94.515 0.254 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.0 -87: (ns/day) (hour/ns) -87: Performance: 245.893 0.098 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (93 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.3 -87: (ns/day) (hour/ns) -87: Performance: 235.321 0.102 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 196.6 -87: (ns/day) (hour/ns) -87: Performance: 307.315 0.078 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 197.9 -87: (ns/day) (hour/ns) -87: Performance: 317.843 0.076 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Last energy frame read 4 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 199.269 0.120 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 198.4 -87: (ns/day) (hour/ns) -87: Performance: 232.392 0.103 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.4 -87: (ns/day) (hour/ns) -87: Performance: 238.455 0.101 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (62 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 198.3 -87: (ns/day) (hour/ns) -87: Performance: 230.225 0.104 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 197.5 -87: (ns/day) (hour/ns) -87: Performance: 318.204 0.075 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.008 0.004 195.6 -87: (ns/day) (hour/ns) -87: Performance: 347.448 0.069 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.0 -87: (ns/day) (hour/ns) -87: Performance: 238.045 0.101 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.1 -87: (ns/day) (hour/ns) -87: Performance: 242.954 0.099 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.1 -87: (ns/day) (hour/ns) -87: Performance: 225.403 0.106 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (61 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.3 -87: (ns/day) (hour/ns) -87: Performance: 237.778 0.101 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 197.7 -87: (ns/day) (hour/ns) -87: Performance: 285.140 0.084 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 207.424 0.116 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.1 -87: (ns/day) (hour/ns) -87: Performance: 237.361 0.101 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.035 0.018 199.3 -87: (ns/day) (hour/ns) -87: Performance: 83.013 0.289 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 198.8 -87: (ns/day) (hour/ns) -87: Performance: 142.628 0.168 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (81 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 198.2 -87: (ns/day) (hour/ns) -87: Performance: 179.690 0.134 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.005 197.8 -87: (ns/day) (hour/ns) -87: Performance: 276.570 0.087 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 197.5 -87: (ns/day) (hour/ns) -87: Performance: 307.860 0.078 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: odicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 4 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.006 197.8 -87: (ns/day) (hour/ns) -87: Performance: 231.375 0.104 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.027 0.013 199.1 -87: (ns/day) (hour/ns) -87: Performance: 109.904 0.218 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -87: 1 -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 199.2 -87: (ns/day) (hour/ns) -87: Performance: 86.054 0.279 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (85 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.035 0.017 199.4 -87: (ns/day) (hour/ns) -87: Performance: 84.572 0.284 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 199.4 -87: (ns/day) (hour/ns) -87: Performance: 85.424 0.281 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Last energy frame read 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.032 0.016 199.1 -87: (ns/day) (hour/ns) -87: Performance: 92.041 0.261 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.048 0.024 199.6 -87: (ns/day) (hour/ns) -87: Performance: 61.068 0.393 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: odicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.5 -87: (ns/day) (hour/ns) -87: Performance: 220.234 0.109 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 49 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.036 0.018 199.5 -87: (ns/day) (hour/ns) -87: Performance: 81.052 0.296 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (128 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.037 0.018 199.4 -87: (ns/day) (hour/ns) -87: Performance: 79.896 0.300 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.032 0.016 199.3 -87: (ns/day) (hour/ns) -87: Performance: 91.568 0.262 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 50 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.629 0.314 199.9 -87: (ns/day) (hour/ns) -87: Performance: 4.672 5.137 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 211.269 0.114 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.3 -87: (ns/day) (hour/ns) -87: Performance: 201.310 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 220.573 0.109 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (527 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.7 -87: (ns/day) (hour/ns) -87: Performance: 191.038 0.126 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.005 198.0 -87: (ns/day) (hour/ns) -87: Performance: 267.608 0.090 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 198.3 -87: (ns/day) (hour/ns) -87: Performance: 236.273 0.102 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 201.917 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 198.0 -87: (ns/day) (hour/ns) -87: Performance: 201.679 0.119 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 198.8 -87: (ns/day) (hour/ns) -87: Performance: 160.587 0.149 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (72 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 198.7 -87: (ns/day) (hour/ns) -87: Performance: 192.576 0.125 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.004 197.5 -87: (ns/day) (hour/ns) -87: Performance: 339.296 0.071 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.009 0.005 196.4 -87: (ns/day) (hour/ns) -87: Performance: 305.456 0.079 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 48 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 198.4 -87: (ns/day) (hour/ns) -87: Performance: 221.812 0.108 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 198.1 -87: (ns/day) (hour/ns) -87: Performance: 266.652 0.090 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: NOTE: 47 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.011 0.006 197.9 -87: (ns/day) (hour/ns) -87: Performance: 259.475 0.092 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (62 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: There were 3 NOTEs -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.3%. -87: The balanceable part of the MD step is 59%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.8%. -87: -87: -87: NOTE: 43 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 196.7 -87: (ns/day) (hour/ns) -87: Performance: 239.093 0.100 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: -87: There were 3 NOTEs -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 3.8%. -87: The balanceable part of the MD step is 58%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.2%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 42 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 195.1 -87: (ns/day) (hour/ns) -87: Performance: 288.864 0.083 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 4. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 4. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.4%. -87: The balanceable part of the MD step is 50%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.2%. -87: -87: -87: NOTE: 43 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.010 0.005 195.9 -87: (ns/day) (hour/ns) -87: Performance: 297.951 0.081 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.7%. -87: The balanceable part of the MD step is 47%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.3%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 196.2 -87: (ns/day) (hour/ns) -87: Performance: 183.959 0.130 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 11.7%. -87: The balanceable part of the MD step is 43%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 5.0%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: NOTE: 5.0 % of the available CPU time was lost due to load imbalance -87: in the domain decomposition. -87: You can consider manually changing the decomposition (option -dd); -87: e.g. by using fewer domains along the box dimension in which there is -87: considerable inhomogeneity in the simulated system. -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 196.8 -87: (ns/day) (hour/ns) -87: Performance: 188.848 0.127 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 100. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 100. -87: -87: -87: There were 4 NOTEs -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.3%. -87: The balanceable part of the MD step is 48%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 196.1 -87: (ns/day) (hour/ns) -87: Performance: 180.282 0.133 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (68 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.0%. -87: The balanceable part of the MD step is 60%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 0.6%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.0 -87: (ns/day) (hour/ns) -87: Performance: 157.393 0.152 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 1.9%. -87: The balanceable part of the MD step is 55%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.0%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 195.9 -87: (ns/day) (hour/ns) -87: Performance: 185.451 0.129 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.5%. -87: The balanceable part of the MD step is 57%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.4%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 197.1 -87: (ns/day) (hour/ns) -87: Performance: 144.605 0.166 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.1%. -87: The balanceable part of the MD step is 55%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.2%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 196.5 -87: (ns/day) (hour/ns) -87: Performance: 156.378 0.153 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.0%. -87: The balanceable part of the MD step is 53%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.008 196.1 -87: (ns/day) (hour/ns) -87: Performance: 173.386 0.138 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: -87: There was 1 WARNING -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.8%. -87: The balanceable part of the MD step is 55%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: NOTE: 46 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 197.0 -87: (ns/day) (hour/ns) -87: Performance: 138.838 0.173 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (88 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was turned on during the run due to measured imbalance. -87: Average load imbalance: 3.2%. -87: The balanceable part of the MD step is 63%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 2.0%. -87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 197.4 -87: (ns/day) (hour/ns) -87: Performance: 139.293 0.172 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.4%. -87: The balanceable part of the MD step is 62%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.5%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.015 0.008 196.1 -87: (ns/day) (hour/ns) -87: Performance: 188.784 0.127 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 2.0%. -87: The balanceable part of the MD step is 54%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.1%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 196.9 -87: (ns/day) (hour/ns) -87: Performance: 156.920 0.153 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.6%. -87: The balanceable part of the MD step is 49%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 196.8 -87: (ns/day) (hour/ns) -87: Performance: 157.216 0.153 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.5%. -87: The balanceable part of the MD step is 49%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.7%. -87: -87: -87: NOTE: 45 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 196.5 -87: (ns/day) (hour/ns) -87: Performance: 169.208 0.142 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: -87: NVE simulation: will use the initial temperature of 68.810 K for -87: determining the Verlet buffer size -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Can not increase nstlist because an NVE ensemble is used -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: -87: Dynamic load balancing report: -87: DLB was off during the run due to low measured imbalance. -87: Average load imbalance: 3.6%. -87: The balanceable part of the MD step is 53%, load imbalance is computed from this. -87: Part of the total run time spent waiting due to load imbalance: 1.9%. -87: -87: -87: NOTE: 44 % of the run time was spent communicating energies, -87: you might want to increase some nst* mdp options -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.008 196.4 -87: (ns/day) (hour/ns) -87: Performance: 173.252 0.139 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (86 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.038 0.019 198.2 -87: (ns/day) (hour/ns) -87: Performance: 76.915 0.312 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: There were 2 NOTEs -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.012 0.006 193.9 -87: (ns/day) (hour/ns) -87: Performance: 238.880 0.100 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 odicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.033 0.017 197.8 -87: (ns/day) (hour/ns) -87: Performance: 88.729 0.270 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.042 0.021 198.4 -87: (ns/day) (hour/ns) -87: Performance: 69.316 0.346 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.037 0.018 198.3 -87: (ns/day) (hour/ns) -87: Performance: 79.769 0.301 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.038 0.019 198.4 -87: (ns/day) (hour/ns) -87: Performance: 75.813 0.317 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (133 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.036 0.018 197.9 -87: (ns/day) (hour/ns) -87: Performance: 81.459 0.295 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.050 0.025 198.8 -87: (ns/day) (hour/ns) -87: Performance: 58.063 0.413 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.037 0.019 198.2 -87: (ns/day) (hour/ns) -87: Performance: 78.608 0.305 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.036 0.018 198.7 -87: (ns/day) (hour/ns) -87: Performance: 81.672 0.294 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.034 0.017 197.9 -87: (ns/day) (hour/ns) -87: Performance: 86.744 0.277 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: -87: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: -87: The Berendsen barostat does not generate any strictly correct ensemble, -87: and should not be used for new production simulations (in our opinion). -87: We recommend using the C-rescale barostat instead. -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: -87: There were 2 NOTEs -87: -87: There was 1 WARNING -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.029 0.015 198.4 -87: (ns/day) (hour/ns) -87: Performance: 99.035 0.242 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (145 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.3 -87: (ns/day) (hour/ns) -87: Performance: 157.800 0.152 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 196.6 -87: (ns/day) (hour/ns) -87: Performance: 214.992 0.112 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.013 0.007 196.6 -87: (ns/day) (hour/ns) -87: Performance: 215.097 0.112 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 197.0 -87: (ns/day) (hour/ns) -87: Performance: 147.286 0.163 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 197.2 -87: (ns/day) (hour/ns) -87: Performance: 166.047 0.145 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 196.5 -87: (ns/day) (hour/ns) -87: Performance: 169.177 0.142 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (77 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.6 -87: (ns/day) (hour/ns) -87: Performance: 162.349 0.148 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.022 0.011 198.0 -87: (ns/day) (hour/ns) -87: Performance: 130.669 0.184 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 196.8 -87: (ns/day) (hour/ns) -87: Performance: 213.413 0.112 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.030 0.015 198.3 -87: (ns/day) (hour/ns) -87: Performance: 96.192 0.250 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.017 0.009 197.1 -87: (ns/day) (hour/ns) -87: Performance: 170.484 0.141 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 3 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.023 0.012 197.9 -87: (ns/day) (hour/ns) -87: Performance: 124.672 0.193 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (97 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.024 0.012 198.0 -87: (ns/day) (hour/ns) -87: Performance: 119.293 0.201 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 4 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 195.1 -87: (ns/day) (hour/ns) -87: Performance: 178.858 0.134 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 197.0 -87: (ns/day) (hour/ns) -87: Performance: 185.622 0.129 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 197.7 -87: (ns/day) (hour/ns) -87: Performance: 136.125 0.176 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.019 0.010 197.2 -87: (ns/day) (hour/ns) -87: Performance: 151.202 0.159 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: -87: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: MTTK coupling is deprecated and will soon be removed -87: -87: -87: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: for current Trotter decomposition methods with vv, nsttcouple and -87: nstpcouple must be equal. Both have been reset to -87: min(nsttcouple,nstpcouple) = 2 -87: -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: -87: COM removal frequency is set to (5). -87: Other settings require a global communication frequency of 2. -87: Note that this will require additional global communication steps, -87: which will reduce performance when using multiple ranks. -87: Consider setting nstcomm to a multiple of 2. -87: -87: -87: There were 5 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.023 0.012 197.6 -87: (ns/day) (hour/ns) -87: Performance: 125.289 0.192 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (92 ms) -87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.020 0.010 197.9 -87: (ns/day) (hour/ns) -87: Performance: 144.554 0.166 -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (1) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.014 0.007 196.4 -87: (ns/day) (hour/ns) -87: Performance: 209.869 0.114 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: Setting nstcalcenergy (100) equal to nstenergy (4) -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 197.3 -87: (ns/day) (hour/ns) -87: Performance: 176.711 0.136 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: There were 2 NOTEs -87: -87: This run will generate roughly 0 Mb of data -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.016 0.008 197.1 -87: (ns/day) (hour/ns) -87: Performance: 176.355 0.136 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.018 0.009 197.3 -87: (ns/day) (hour/ns) -87: Performance: 160.311 0.150 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: -87: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -87: that with the Verlet scheme, nstlist has no effect on the accuracy of -87: your simulation. -87: -87: -87: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: -87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -87: setting nstcomm equal to nstcalcenergy for less overhead -87: -87: Generated 1 of the 1 non-bonded parameter combinations -87: -87: Excluding 1 bonded neighbours molecule type 'Argon' -87: -87: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon12.gro' -87: Number of degrees of freedom in T-Coupling group System is 33.00 -87: -87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K -87: -87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm -87: -87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm -87: -87: Note that mdrun will redetermine rlist based on the actual pair-list setup -87: -87: This run will generate roughly 0 Mb of data -87: -87: There were 2 NOTEs -87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -87: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 -87: -87: Using 2 MPI processes -87: Using 1 OpenMP thread per MPI process -87: -87: -87: NOTE: The number of threads is not equal to the number of (logical) cpus -87: and the -pin option is set to auto: will not pin threads to cpus. -87: This can lead to significant performance degradation. -87: Consider using -pin on (and -pinoffset in case you run multiple jobs). -87: starting mdrun 'Argon' -87: 16 steps, 0.0 ps. -87: -87: Writing final coordinates. -87: -87: Core t (s) Wall t (s) (%) -87: Time: 0.021 0.011 197.7 -87: (ns/day) (hour/ns) -87: Performance: 136.645 0.176 -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file -87: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file -87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (82 ms) -87: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4313 ms total) -87: -87: [----------] Global test environment tear-down -87: [==========] 25 tests from 1 test suite ran. (4345 ms total) -87: [ PASSED ] 25 tests. -87/96 Test #87: MdrunCoordinationCouplingTests2Ranks ......... Passed 4.62 sec -test 88 - Start 88: MdrunCoordinationConstraintsTests1Rank - -88: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" -88: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -88: Test timeout computed to be: 1920 -88: [==========] Running 13 tests from 1 test suite. -88: [----------] Global test environment set-up. -88: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.022 0.022 99.8 -88: (ns/day) (hour/ns) -88: Performance: 65.320 0.367 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.3 -88: (ns/day) (hour/ns) -88: Performance: 254.307 0.094 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 4. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 4. -88: -88: -88: There were 5 NOTEs -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.010 0.010 99.6 -88: (ns/day) (hour/ns) -88: Performance: 144.788 0.166 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 5 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.011 0.011 99.7 -88: (ns/day) (hour/ns) -88: Performance: 129.809 0.185 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.5 -88: (ns/day) (hour/ns) -88: Performance: 180.949 0.133 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 222.476 0.108 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1370 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.010 0.010 99.4 -88: (ns/day) (hour/ns) -88: Performance: 141.062 0.170 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.005 0.005 98.9 -88: (ns/day) (hour/ns) -88: Performance: 307.799 0.078 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.005 0.005 98.9 -88: (ns/day) (hour/ns) -88: Performance: 305.312 0.079 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.013 0.013 99.5 -88: (ns/day) (hour/ns) -88: Performance: 115.553 0.208 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.0 -88: (ns/day) (hour/ns) -88: Performance: 246.335 0.097 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.0 -88: (ns/day) (hour/ns) -88: Performance: 236.864 0.101 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1334 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.010 0.010 99.4 -88: (ns/day) (hour/ns) -88: Performance: 146.065 0.164 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 213.724 0.112 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.2 -88: (ns/day) (hour/ns) -88: Performance: 260.987 0.092 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 98.9 -88: (ns/day) (hour/ns) -88: Performance: 240.263 0.100 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.2 -88: (ns/day) (hour/ns) -88: Performance: 190.107 0.126 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.3 -88: (ns/day) (hour/ns) -88: Performance: 219.700 0.109 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1331 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.1 -88: (ns/day) (hour/ns) -88: Performance: 242.276 0.099 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.355 0.355 100.0 -88: (ns/day) (hour/ns) -88: Performance: 4.142 5.794 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.790 0.790 100.0 -88: (ns/day) (hour/ns) -88: Performance: 1.858 12.914 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.016 0.017 99.7 -88: (ns/day) (hour/ns) -88: Performance: 88.922 0.270 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.4 -88: (ns/day) (hour/ns) -88: Performance: 159.887 0.150 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 168.295 0.143 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3001 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.4 -88: (ns/day) (hour/ns) -88: Performance: 158.529 0.151 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 210.792 0.114 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.014 0.014 99.7 -88: (ns/day) (hour/ns) -88: Performance: 103.288 0.232 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.010 0.010 99.5 -88: (ns/day) (hour/ns) -88: Performance: 150.674 0.159 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.020 0.020 99.8 -88: (ns/day) (hour/ns) -88: Performance: 73.824 0.325 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.2 -88: (ns/day) (hour/ns) -88: Performance: 229.428 0.105 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1366 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.3 -88: (ns/day) (hour/ns) -88: Performance: 185.275 0.130 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.005 0.005 99.2 -88: (ns/day) (hour/ns) -88: Performance: 301.679 0.080 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.005 0.005 99.2 -88: (ns/day) (hour/ns) -88: Performance: 306.056 0.078 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 172.590 0.139 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 163.376 0.147 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 205.744 0.117 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1338 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.030 0.030 99.8 -88: (ns/day) (hour/ns) -88: Performance: 49.146 0.488 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.4 -88: (ns/day) (hour/ns) -88: Performance: 228.704 0.105 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 4. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 4. -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.005 0.005 99.1 -88: (ns/day) (hour/ns) -88: Performance: 287.006 0.084 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 166.498 0.144 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 4 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.1 -88: (ns/day) (hour/ns) -88: Performance: 230.570 0.104 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.6 -88: (ns/day) (hour/ns) -88: Performance: 156.321 0.154 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1371 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 162.138 0.148 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.4 -88: (ns/day) (hour/ns) -88: Performance: 193.559 0.124 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 207.239 0.116 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.010 0.010 99.6 -88: (ns/day) (hour/ns) -88: Performance: 147.020 0.163 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.007 99.2 -88: (ns/day) (hour/ns) -88: Performance: 225.688 0.106 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.6 -88: (ns/day) (hour/ns) -88: Performance: 159.737 0.150 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1359 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 219.363 0.109 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.004 0.004 99.2 -88: (ns/day) (hour/ns) -88: Performance: 332.448 0.072 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.004 0.004 99.2 -88: (ns/day) (hour/ns) -88: Performance: 334.143 0.072 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.007 99.5 -88: (ns/day) (hour/ns) -88: Performance: 225.456 0.106 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.4 -88: (ns/day) (hour/ns) -88: Performance: 239.842 0.100 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.006 0.006 99.1 -88: (ns/day) (hour/ns) -88: Performance: 240.498 0.100 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1315 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.7 -88: (ns/day) (hour/ns) -88: Performance: 165.550 0.145 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.7 -88: (ns/day) (hour/ns) -88: Performance: 183.051 0.131 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 4. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 4. -88: -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.1 -88: (ns/day) (hour/ns) -88: Performance: 217.251 0.110 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.6 -88: (ns/day) (hour/ns) -88: Performance: 156.710 0.153 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.6 -88: (ns/day) (hour/ns) -88: Performance: 199.708 0.120 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 100. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 100. -88: -88: -88: There were 5 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.7 -88: (ns/day) (hour/ns) -88: Performance: 168.774 0.142 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1333 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.6 -88: (ns/day) (hour/ns) -88: Performance: 168.322 0.143 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.024 0.025 99.8 -88: (ns/day) (hour/ns) -88: Performance: 59.830 0.401 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.3 -88: (ns/day) (hour/ns) -88: Performance: 219.833 0.109 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.6 -88: (ns/day) (hour/ns) -88: Performance: 176.254 0.136 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.6 -88: (ns/day) (hour/ns) -88: Performance: 180.673 0.133 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: NVE simulation: will use the initial temperature of 398.997 K for -88: determining the Verlet buffer size -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Can not increase nstlist because an NVE ensemble is used -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.011 0.011 99.7 -88: (ns/day) (hour/ns) -88: Performance: 130.369 0.184 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1336 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.009 0.009 99.5 -88: (ns/day) (hour/ns) -88: Performance: 171.242 0.140 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.013 0.013 99.7 -88: (ns/day) (hour/ns) -88: Performance: 112.792 0.213 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.014 0.014 99.7 -88: (ns/day) (hour/ns) -88: Performance: 104.954 0.229 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.028 0.028 99.8 -88: (ns/day) (hour/ns) -88: Performance: 51.604 0.465 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.018 0.018 99.7 -88: (ns/day) (hour/ns) -88: Performance: 80.521 0.298 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -88: COM removal frequency is set to (5). -88: Other settings require a global communication frequency of 2. -88: Note that this will require additional global communication steps, -88: which will reduce performance when using multiple ranks. -88: Consider setting nstcomm to a multiple of 2. -88: -88: -88: There were 4 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.018 0.018 99.8 -88: (ns/day) (hour/ns) -88: Performance: 80.924 0.297 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1382 ms) -88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.026 0.026 99.9 -88: (ns/day) (hour/ns) -88: Performance: 56.939 0.422 -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (1) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.017 0.017 99.8 -88: (ns/day) (hour/ns) -88: Performance: 84.460 0.284 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: Setting nstcalcenergy (100) equal to nstenergy (4) -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.007 0.007 99.4 -88: (ns/day) (hour/ns) -88: Performance: 198.665 0.121 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.008 0.008 99.3 -88: (ns/day) (hour/ns) -88: Performance: 186.826 0.128 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: -88: This run will generate roughly 0 Mb of data -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.028 0.029 99.8 -88: (ns/day) (hour/ns) -88: Performance: 51.476 0.466 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -88: -88: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -88: that with the Verlet scheme, nstlist has no effect on the accuracy of -88: your simulation. -88: -88: -88: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -88: setting nstcomm equal to nstcalcenergy for less overhead -88: -88: Generated 330891 of the 330891 non-bonded parameter combinations -88: Generating 1-4 interactions: fudge = 0.5 -88: -88: Generated 330891 of the 330891 1-4 parameter combinations -88: -88: Excluding 2 bonded neighbours molecule type 'SOL' -88: -88: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -88: Number of degrees of freedom in T-Coupling group System is 27.00 -88: -88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -88: -88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -88: -88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -88: -88: Note that mdrun will redetermine rlist based on the actual pair-list setup -88: -88: This run will generate roughly 0 Mb of data -88: -88: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -88: You are using a plain Coulomb cut-off, which might produce artifacts. -88: You might want to consider using PME electrostatics. -88: -88: -88: -88: There were 3 NOTEs -88: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -88: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -88: -88: Using 1 MPI process -88: Using 1 OpenMP thread -88: -88: -88: NOTE: Thread affinity was not set. -88: starting mdrun 'spc2' -88: 16 steps, 0.0 ps. -88: -88: Writing final coordinates. -88: -88: Core t (s) Wall t (s) (%) -88: Time: 0.014 0.014 99.7 -88: (ns/day) (hour/ns) -88: Performance: 106.836 0.225 -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -88: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1378 ms) -88: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (19221 ms total) -88: -88: [----------] Global test environment tear-down -88: [==========] 13 tests from 1 test suite ran. (19242 ms total) -88: [ PASSED ] 13 tests. -88/96 Test #88: MdrunCoordinationConstraintsTests1Rank ....... Passed 19.51 sec -test 89 - Start 89: MdrunCoordinationConstraintsTests2Ranks - -89: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" -89: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -89: Test timeout computed to be: 1920 -89: [==========] Running 13 tests from 1 test suite. -89: [----------] Global test environment set-up. -89: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.6%. -89: The balanceable part of the MD step is 51%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.3%. -89: -89: -89: NOTE: 44 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 198.1 -89: (ns/day) (hour/ns) -89: Performance: 221.127 0.109 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.7%. -89: The balanceable part of the MD step is 46%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.3%. -89: -89: -89: NOTE: 44 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 196.7 -89: (ns/day) (hour/ns) -89: Performance: 286.839 0.084 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 4. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 4. -89: -89: -89: There were 5 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.5%. -89: The balanceable part of the MD step is 37%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.6%. -89: -89: -89: NOTE: 44 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.009 0.005 197.2 -89: (ns/day) (hour/ns) -89: Performance: 313.908 0.076 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.8%. -89: The balanceable part of the MD step is 31%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.6%. -89: -89: -89: NOTE: 45 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 196.8 -89: (ns/day) (hour/ns) -89: Performance: 218.604 0.110 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 4.4%. -89: The balanceable part of the MD step is 32%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.4%. -89: -89: -89: NOTE: 45 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.011 0.006 196.5 -89: (ns/day) (hour/ns) -89: Performance: 258.436 0.093 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.0%. -89: The balanceable part of the MD step is 35%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.4%. -89: -89: -89: NOTE: 46 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.006 198.0 -89: (ns/day) (hour/ns) -89: Performance: 226.106 0.106 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1326 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.6%. -89: The balanceable part of the MD step is 48%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.8%. -89: -89: -89: NOTE: 45 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.020 0.010 197.8 -89: (ns/day) (hour/ns) -89: Performance: 143.246 0.168 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.3%. -89: The balanceable part of the MD step is 46%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.0%. -89: -89: -89: NOTE: 42 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 196.1 -89: (ns/day) (hour/ns) -89: Performance: 278.741 0.086 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB got disabled because it was unsuitable to use. -89: Average load imbalance: 5.5%. -89: The balanceable part of the MD step is 40%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 2.2%. -89: -89: -89: NOTE: 44 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.012 0.006 196.6 -89: (ns/day) (hour/ns) -89: Performance: 245.271 0.098 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 3.4%. -89: The balanceable part of the MD step is 38%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.3%. -89: -89: -89: NOTE: 46 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.007 197.8 -89: (ns/day) (hour/ns) -89: Performance: 200.188 0.120 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 4.0%. -89: The balanceable part of the MD step is 39%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.5%. -89: -89: -89: NOTE: 46 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.6 -89: (ns/day) (hour/ns) -89: Performance: 203.632 0.118 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.7%. -89: The balanceable part of the MD step is 38%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.0%. -89: -89: -89: NOTE: 45 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.006 197.2 -89: (ns/day) (hour/ns) -89: Performance: 226.347 0.106 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1335 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.5%. -89: The balanceable part of the MD step is 47%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.2%. -89: -89: -89: NOTE: 47 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.030 0.015 198.7 -89: (ns/day) (hour/ns) -89: Performance: 96.786 0.248 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.0%. -89: The balanceable part of the MD step is 45%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.5%. -89: -89: -89: NOTE: 43 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.011 0.005 197.5 -89: (ns/day) (hour/ns) -89: Performance: 274.286 0.088 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Last energy frame read 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 3.4%. -89: The balanceable part of the MD step is 40%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.4%. -89: -89: -89: NOTE: 43 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 196.1 -89: (ns/day) (hour/ns) -89: Performance: 296.875 0.081 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.1%. -89: The balanceable part of the MD step is 40%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.8%. -89: -89: -89: NOTE: 47 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.019 0.010 198.6 -89: (ns/day) (hour/ns) -89: Performance: 153.028 0.157 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.9%. -89: The balanceable part of the MD step is 37%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.7%. -89: -89: -89: NOTE: 47 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.024 0.012 198.2 -89: (ns/day) (hour/ns) -89: Performance: 119.534 0.201 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.2%. -89: The balanceable part of the MD step is 39%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.9%. -89: -89: -89: NOTE: 45 % of the run time was spent communicating energies, -89: you might want to increase some nst* mdp options -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 196.9 -89: (ns/day) (hour/ns) -89: Performance: 216.450 0.111 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1341 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.023 0.012 198.3 -89: (ns/day) (hour/ns) -89: Performance: 127.415 0.188 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 195.7 -89: (ns/day) (hour/ns) -89: Performance: 285.100 0.084 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 196.9 -89: (ns/day) (hour/ns) -89: Performance: 287.831 0.083 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 4 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.2 -89: (ns/day) (hour/ns) -89: Performance: 202.458 0.119 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.2 -89: (ns/day) (hour/ns) -89: Performance: 204.095 0.118 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.022 0.011 198.2 -89: (ns/day) (hour/ns) -89: Performance: 129.896 0.185 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1341 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.0 -89: (ns/day) (hour/ns) -89: Performance: 210.428 0.114 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.012 0.006 196.6 -89: (ns/day) (hour/ns) -89: Performance: 240.474 0.100 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Last energy frame read 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 196.6 -89: (ns/day) (hour/ns) -89: Performance: 279.076 0.086 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 198.4 -89: (ns/day) (hour/ns) -89: Performance: 189.764 0.126 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 197.2 -89: (ns/day) (hour/ns) -89: Performance: 176.769 0.136 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 197.1 -89: (ns/day) (hour/ns) -89: Performance: 195.658 0.123 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1316 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.0 -89: (ns/day) (hour/ns) -89: Performance: 201.307 0.119 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.012 0.006 196.0 -89: (ns/day) (hour/ns) -89: Performance: 243.430 0.099 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.011 0.006 195.9 -89: (ns/day) (hour/ns) -89: Performance: 255.494 0.094 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 196.6 -89: (ns/day) (hour/ns) -89: Performance: 215.979 0.111 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.7 -89: (ns/day) (hour/ns) -89: Performance: 211.832 0.113 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.006 196.7 -89: (ns/day) (hour/ns) -89: Performance: 228.483 0.105 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1328 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.2 -89: (ns/day) (hour/ns) -89: Performance: 204.240 0.118 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.010 0.005 197.6 -89: (ns/day) (hour/ns) -89: Performance: 280.575 0.086 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 4. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 4. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.009 0.005 197.4 -89: (ns/day) (hour/ns) -89: Performance: 315.063 0.076 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.018 0.009 197.2 -89: (ns/day) (hour/ns) -89: Performance: 162.497 0.148 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 197.3 -89: (ns/day) (hour/ns) -89: Performance: 200.730 0.120 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.012 0.006 197.5 -89: (ns/day) (hour/ns) -89: Performance: 238.395 0.101 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1336 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 197.5 -89: (ns/day) (hour/ns) -89: Performance: 195.664 0.123 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.037 0.019 199.1 -89: (ns/day) (hour/ns) -89: Performance: 78.399 0.306 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.009 0.005 197.7 -89: (ns/day) (hour/ns) -89: Performance: 310.506 0.077 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 198.5 -89: (ns/day) (hour/ns) -89: Performance: 185.778 0.129 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.006 198.0 -89: (ns/day) (hour/ns) -89: Performance: 230.182 0.104 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.006 198.1 -89: (ns/day) (hour/ns) -89: Performance: 229.689 0.104 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1323 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 198.5 -89: (ns/day) (hour/ns) -89: Performance: 194.565 0.123 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.012 0.006 198.3 -89: (ns/day) (hour/ns) -89: Performance: 241.086 0.100 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.017 0.009 198.6 -89: (ns/day) (hour/ns) -89: Performance: 169.966 0.141 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 1 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 198.3 -89: (ns/day) (hour/ns) -89: Performance: 221.373 0.108 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 197.5 -89: (ns/day) (hour/ns) -89: Performance: 192.672 0.125 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 197.3 -89: (ns/day) (hour/ns) -89: Performance: 216.146 0.111 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1288 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.3%. -89: The balanceable part of the MD step is 58%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.7%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.019 0.010 197.1 -89: (ns/day) (hour/ns) -89: Performance: 149.319 0.161 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.0%. -89: The balanceable part of the MD step is 56%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.1%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 195.8 -89: (ns/day) (hour/ns) -89: Performance: 218.321 0.110 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 4. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 4. -89: -89: -89: There were 5 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.4%. -89: The balanceable part of the MD step is 51%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.2%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 195.7 -89: (ns/day) (hour/ns) -89: Performance: 190.539 0.126 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 2.8%. -89: The balanceable part of the MD step is 44%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 1.2%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.019 0.009 196.7 -89: (ns/day) (hour/ns) -89: Performance: 155.880 0.154 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.6%. -89: The balanceable part of the MD step is 46%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.7%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.026 0.013 197.3 -89: (ns/day) (hour/ns) -89: Performance: 111.854 0.215 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 100. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 100. -89: -89: -89: There were 5 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB got disabled because it was unsuitable to use. -89: Average load imbalance: 5.0%. -89: The balanceable part of the MD step is 48%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 2.4%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.015 0.008 195.9 -89: (ns/day) (hour/ns) -89: Performance: 187.940 0.128 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1298 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.6%. -89: The balanceable part of the MD step is 54%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.3%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.021 0.011 197.2 -89: (ns/day) (hour/ns) -89: Performance: 138.907 0.173 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.1%. -89: The balanceable part of the MD step is 56%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.6%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.013 0.007 195.2 -89: (ns/day) (hour/ns) -89: Performance: 215.003 0.112 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 9 time 0.009 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 1.2%. -89: The balanceable part of the MD step is 52%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.6%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.033 0.017 198.0 -89: (ns/day) (hour/ns) -89: Performance: 87.803 0.273 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.4%. -89: The balanceable part of the MD step is 50%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.2%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.021 0.010 196.7 -89: (ns/day) (hour/ns) -89: Performance: 139.990 0.171 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.8%. -89: The balanceable part of the MD step is 51%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.4%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 196.5 -89: (ns/day) (hour/ns) -89: Performance: 182.750 0.131 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: NVE simulation: will use the initial temperature of 398.997 K for -89: determining the Verlet buffer size -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Can not increase nstlist because an NVE ensemble is used -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: -89: Dynamic load balancing report: -89: DLB was off during the run due to low measured imbalance. -89: Average load imbalance: 0.6%. -89: The balanceable part of the MD step is 51%, load imbalance is computed from this. -89: Part of the total run time spent waiting due to load imbalance: 0.3%. -89: -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 196.3 -89: (ns/day) (hour/ns) -89: Performance: 175.751 0.137 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1322 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.017 0.009 197.0 -89: (ns/day) (hour/ns) -89: Performance: 169.496 0.142 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 196.3 -89: (ns/day) (hour/ns) -89: Performance: 205.367 0.117 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.014 0.007 194.9 -89: (ns/day) (hour/ns) -89: Performance: 205.937 0.117 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 195.5 -89: (ns/day) (hour/ns) -89: Performance: 181.881 0.132 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 195.7 -89: (ns/day) (hour/ns) -89: Performance: 177.493 0.135 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: -89: COM removal frequency is set to (5). -89: Other settings require a global communication frequency of 2. -89: Note that this will require additional global communication steps, -89: which will reduce performance when using multiple ranks. -89: Consider setting nstcomm to a multiple of 2. -89: -89: -89: There were 4 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 195.7 -89: (ns/day) (hour/ns) -89: Performance: 179.397 0.134 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1327 ms) -89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 196.0 -89: (ns/day) (hour/ns) -89: Performance: 175.258 0.137 -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (1) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.016 0.008 196.0 -89: (ns/day) (hour/ns) -89: Performance: 178.591 0.134 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: Setting nstcalcenergy (100) equal to nstenergy (4) -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.022 0.011 197.2 -89: (ns/day) (hour/ns) -89: Performance: 134.555 0.178 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.023 0.012 195.5 -89: (ns/day) (hour/ns) -89: Performance: 122.851 0.195 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: There were 3 NOTEs -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.021 0.011 196.7 -89: (ns/day) (hour/ns) -89: Performance: 136.809 0.175 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: -89: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -89: that with the Verlet scheme, nstlist has no effect on the accuracy of -89: your simulation. -89: -89: -89: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider -89: setting nstcomm equal to nstcalcenergy for less overhead -89: -89: Generated 330891 of the 330891 non-bonded parameter combinations -89: Generating 1-4 interactions: fudge = 0.5 -89: -89: Generated 330891 of the 330891 1-4 parameter combinations -89: -89: Excluding 2 bonded neighbours molecule type 'SOL' -89: -89: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/tip3p5.gro' -89: Number of degrees of freedom in T-Coupling group System is 27.00 -89: -89: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: -89: You are using a plain Coulomb cut-off, which might produce artifacts. -89: You might want to consider using PME electrostatics. -89: -89: -89: -89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -89: -89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm -89: -89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm -89: -89: Note that mdrun will redetermine rlist based on the actual pair-list setup -89: -89: This run will generate roughly 0 Mb of data -89: -89: There were 3 NOTEs -89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -89: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 -89: -89: Using 2 MPI processes -89: Using 1 OpenMP thread per MPI process -89: -89: -89: NOTE: The number of threads is not equal to the number of (logical) cpus -89: and the -pin option is set to auto: will not pin threads to cpus. -89: This can lead to significant performance degradation. -89: Consider using -pin on (and -pinoffset in case you run multiple jobs). -89: starting mdrun 'spc2' -89: 16 steps, 0.0 ps. -89: -89: Writing final coordinates. -89: -89: Core t (s) Wall t (s) (%) -89: Time: 0.017 0.009 196.2 -89: (ns/day) (hour/ns) -89: Performance: 170.051 0.141 -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file -89: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file -89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1337 ms) -89: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (17225 ms total) -89: -89: [----------] Global test environment tear-down -89: [==========] 13 tests from 1 test suite ran. (17274 ms total) -89: [ PASSED ] 13 tests. -89/96 Test #89: MdrunCoordinationConstraintsTests2Ranks ...... Passed 17.55 sec -test 90 - Start 90: MdrunFEPTests - -90: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunFEPTests.xml" -90: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -90: Test timeout computed to be: 600 -90: [==========] Running 14 tests from 2 test suites. -90: [----------] Global test environment set-up. -90: [----------] 2 tests from ExpandedEnsembleTest -90: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 79.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: -90: You are using a plain Coulomb cut-off, which might produce artifacts. -90: You might want to consider using PME electrostatics. -90: -90: -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun '30 atom system in water' -90: 16 steps, 0.0 ps. -90: Generated 2485 of the 2485 non-bonded parameter combinations -90: -90: Generated 2485 of the 2485 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'nonanol' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -90: -90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.030 0.015 199.5 -90: (ns/day) (hour/ns) -90: Performance: 97.112 0.247 -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps -90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -90: -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun '30 atom system in water' -90: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.022 0.011 198.7 -90: (ns/day) (hour/ns) -90: Performance: 70.304 0.341 -90: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (53 ms) -90: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -90: that with the Verlet scheme, nstlist has no effect on the accuracy of -90: your simulation. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 79.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: -90: You are using a plain Coulomb cut-off, which might produce artifacts. -90: You might want to consider using PME electrostatics. -90: -90: -90: -90: There were 2 NOTEs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun '30 atom system in water' -90: 1 steps, 0.0 ps. -90: Generated 2485 of the 2485 non-bonded parameter combinations -90: -90: Generated 2485 of the 2485 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'nonanol' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' -90: -90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.022 0.011 199.5 -90: (ns/day) (hour/ns) -90: Performance: 15.574 1.541 -90: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (26 ms) -90: [----------] 2 tests from ExpandedEnsembleTest (79 ms total) -90: -90: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 3 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -36741217 -90: -90: Generated 153 of the 153 non-bonded parameter combinations -90: -90: Generated 153 of the 153 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'ASN' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.066 0.033 199.6 -90: (ns/day) (hour/ns) -90: Performance: 55.019 0.436 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) -90: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (250 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 3 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to 2135128044 -90: -90: Generated 153 of the 153 non-bonded parameter combinations -90: -90: Generated 153 of the 153 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'ASN' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.064 0.032 199.5 -90: (ns/day) (hour/ns) -90: Performance: 56.974 0.421 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (116 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -90: With PME there is a minor soft core effect present at the cut-off, -90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -90: energy conservation, but usually other effects dominate. With a common -90: sigma value of 0.34 nm the fraction of the particle-particle potential at -90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 4 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -19572139 -90: -90: Generated 153 of the 153 non-bonded parameter combinations -90: -90: Generated 153 of the 153 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'ASN' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.055 0.028 199.5 -90: (ns/day) (hour/ns) -90: Performance: 65.526 0.366 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (111 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -90: With PME there is a minor soft core effect present at the cut-off, -90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -90: energy conservation, but usually other effects dominate. With a common -90: sigma value of 0.34 nm the fraction of the particle-particle potential at -90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: -90: NOTE 3 [file topol.top, line 155]: -90: System has non-zero total charge: 1.000000 -90: Total charge should normally be an integer. See -90: https://manual.gromacs.org/current/user-guide/floating-point.html -90: for discussion on how close it should be to an integer. -90: -90: -90: -90: -90: WARNING 2 [file topol.top, line 155]: -90: You are using Ewald electrostatics in a system with net charge. This can -90: lead to severe artifacts, such as ions moving into regions with low -90: dielectric, due to the uniform background charge. We suggest to -90: neutralize your system with counter ions, possibly in combination with a -90: physiological salt concentration. -90: -90: Setting the LD random seed to 2132008770 -90: -90: Generated 171 of the 171 non-bonded parameter combinations -90: -90: Generated 171 of the 171 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Excluding 1 bonded neighbours molecule type 'NA' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'ASN' -90: -90: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -90: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -90: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -90: Charge -90: J. Chem. Theory Comput. (2014) -90: DOI: 10.1021/ct400626b -90: -------- -------- --- Thank You --- -------- -------- -90: -90: Number of degrees of freedom in T-Coupling group System is 358.00 -90: -90: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 5 NOTEs -90: -90: There were 2 WARNINGs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: There are: 1 Ion residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.96 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.059 0.030 199.6 -90: (ns/day) (hour/ns) -90: Performance: 61.432 0.391 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (206 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -90: With PME there is a minor soft core effect present at the cut-off, -90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -90: energy conservation, but usually other effects dominate. With a common -90: sigma value of 0.34 nm the fraction of the particle-particle potential at -90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: -90: NOTE 3 [file topol.top, line 165]: -90: System has non-zero total charge: 1.000000 -90: Total charge should normally be an integer. See -90: https://manual.gromacs.org/current/user-guide/floating-point.html -90: for discussion on how close it should be to an integer. -90: -90: -90: -90: -90: WARNING 2 [file topol.top, line 165]: -90: You are using Ewald electrostatics in a system with net charge. This can -90: lead to severe artifacts, such as ions moving into regions with low -90: dielectric, due to the uniform background charge. We suggest to -90: neutralize your system with counter ions, possibly in combination with a -90: physiological salt concentration. -90: -90: Setting the LD random seed to -71438413 -90: -90: Generated 190 of the 190 non-bonded parameter combinations -90: -90: Generated 190 of the 190 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Excluding 1 bonded neighbours molecule type 'NA' -90: -90: turning H bonds into constraints... -90: -90: Excluding 1 bonded neighbours molecule type 'CL' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'CL' -90: -90: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ -90: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof -90: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net -90: Charge -90: J. Chem. Theory Comput. (2014) -90: DOI: 10.1021/ct400626b -90: -------- -------- --- Thank You --- -------- -------- -90: -90: Number of degrees of freedom in T-Coupling group System is 361.00 -90: -90: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 5 NOTEs -90: -90: There were 2 WARNINGs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: There are: 2 Ion residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -90: -90: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.96 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.066 0.033 199.7 -90: (ns/day) (hour/ns) -90: Performance: 54.625 0.439 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (49 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: -90: For proper sampling of the (nearly) decoupled state, stochastic dynamics -90: should be used -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -90: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off -90: and vdw_modifier=Force-switch -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 4 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 100 steps, 0.1 ps. -90: Setting the LD random seed to 2012217087 -90: -90: Generated 153 of the 153 non-bonded parameter combinations -90: -90: Generated 153 of the 153 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Coupling 1 copies of molecule type 'ASN' -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.242 0.121 199.9 -90: (ns/day) (hour/ns) -90: Performance: 72.106 0.333 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (206 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: -90: WARNING 2 [file topol.top, line 72]: -90: No default Bond types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '7 8 1'. -90: -90: -90: WARNING 3 [file topol.top, line 73]: -90: No default Bond types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '7 9 1'. -90: -90: -90: WARNING 4 [file topol.top, line 98]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '6 5 7 1'. -90: -90: -90: WARNING 5 [file topol.top, line 99]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '5 7 8 1'. -90: -90: -90: WARNING 6 [file topol.top, line 100]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '5 7 9 1'. -90: -90: -90: WARNING 7 [file topol.top, line 101]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '8 7 9 1'. -90: -90: -90: WARNING 8 [file topol.top, line 111]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '1 5 7 8 3'. -90: -90: -90: WARNING 9 [file topol.top, line 112]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '1 5 7 9 3'. -90: -90: -90: WARNING 10 [file topol.top, line 113]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '6 5 7 8 3'. -90: -90: -90: WARNING 11 [file topol.top, line 114]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '6 5 7 9 3'. -90: -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 2 NOTEs -90: -90: There were 11 WARNINGs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -54538369 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.085 0.043 199.7 -90: (ns/day) (hour/ns) -90: Performance: 42.435 0.566 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (126 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: -90: WARNING 2 [file topol.top, line 72]: -90: No default Bond types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '7 8 1'. -90: -90: -90: WARNING 3 [file topol.top, line 73]: -90: No default Bond types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '7 9 1'. -90: -90: -90: WARNING 4 [file topol.top, line 98]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '6 5 7 1'. -90: -90: -90: WARNING 5 [file topol.top, line 99]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '5 7 8 1'. -90: -90: -90: WARNING 6 [file topol.top, line 100]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '5 7 9 1'. -90: -90: -90: WARNING 7 [file topol.top, line 101]: -90: No default Angle types for perturbed atoms in interaction, using normal -90: values. The interaction was -90: '8 7 9 1'. -90: -90: -90: WARNING 8 [file topol.top, line 111]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '1 5 7 8 3'. -90: -90: -90: WARNING 9 [file topol.top, line 112]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '1 5 7 9 3'. -90: -90: -90: WARNING 10 [file topol.top, line 113]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '6 5 7 8 3'. -90: -90: -90: WARNING 11 [file topol.top, line 114]: -90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using -90: normal values. The interaction was -90: '6 5 7 9 3'. -90: -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -90: Removing center of mass motion in the presence of position restraints -90: might cause artifacts. When you are using position restraints to -90: equilibrate a macro-molecule, the artifacts are usually negligible. -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 3 NOTEs -90: -90: There were 11 WARNINGs -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -840303106 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.089 0.045 199.7 -90: (ns/day) (hour/ns) -90: Performance: 40.756 0.589 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (128 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 2 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -603979784 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.88 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.035 0.018 199.4 -90: (ns/day) (hour/ns) -90: Performance: 103.295 0.232 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (98 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: There was 1 NOTE -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.021 0.011 198.8 -90: (ns/day) (hour/ns) -90: Performance: 172.691 0.139 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -1160793281 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.88 -90: -90: This run will generate roughly 0 Mb of data -90: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (91 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -90: With PME there is a minor soft core effect present at the cut-off, -90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -90: energy conservation, but usually other effects dominate. With a common -90: sigma value of 0.34 nm the fraction of the particle-particle potential at -90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 3 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -24641 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.94 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.065 0.032 199.7 -90: (ns/day) (hour/ns) -90: Performance: 56.141 0.427 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (114 ms) -90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s -90: -90: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -90: With PME there is a minor soft core effect present at the cut-off, -90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on -90: energy conservation, but usually other effects dominate. With a common -90: sigma value of 0.34 nm the fraction of the particle-particle potential at -90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. -90: -90: -90: WARNING 1 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -90: The Berendsen thermostat does not generate the correct kinetic energy -90: distribution, and should not be used for new production simulations (in -90: our opinion). We would recommend the V-rescale thermostat. -90: -90: Generating 1-4 interactions: fudge = 0.5 -90: Number of degrees of freedom in T-Coupling group System is 355.00 -90: -90: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -90: The optimal PME mesh load for parallel simulations is below 0.5 -90: and for highly parallel simulations between 0.25 and 0.33, -90: for higher performance, increase the cut-off and the PME grid spacing. -90: -90: -90: -90: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: -90: For free energy simulations, the optimal load limit increases from 0.5 to -90: 0.667 -90: -90: -90: -90: There were 3 NOTEs -90: -90: There was 1 WARNING -90: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -90: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -90: Changing nstlist from 10 to 100, rlist from 1 to 1 -90: -90: Using 1 MPI process -90: Using 2 OpenMP threads -90: -90: -90: NOTE: The number of threads is not equal to the number of (logical) cpus -90: and the -pin option is set to auto: will not pin threads to cpus. -90: This can lead to significant performance degradation. -90: Consider using -pin on (and -pinoffset in case you run multiple jobs). -90: starting mdrun 'AA' -90: 20 steps, 0.0 ps. -90: Setting the LD random seed to -8462337 -90: -90: Generated 136 of the 136 non-bonded parameter combinations -90: -90: Generated 136 of the 136 1-4 parameter combinations -90: -90: Excluding 3 bonded neighbours molecule type 'ASN' -90: -90: turning H bonds into constraints... -90: -90: Excluding 2 bonded neighbours molecule type 'SOL' -90: -90: turning H bonds into constraints... -90: -90: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' -90: Analysing residue names: -90: There are: 1 Protein residues -90: There are: 56 Water residues -90: Analysing Protein... -90: -90: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 -90: -90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K -90: -90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm -90: -90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm -90: -90: Note that mdrun will redetermine rlist based on the actual pair-list setup -90: Calculating fourier grid dimensions for X Y Z -90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 -90: -90: Estimate for the relative computational load of the PME mesh part: 0.88 -90: -90: This run will generate roughly 0 Mb of data -90: -90: Writing final coordinates. -90: -90: Core t (s) Wall t (s) (%) -90: Time: 0.039 0.020 199.6 -90: (ns/day) (hour/ns) -90: Performance: 91.828 0.261 -90: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file -90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (101 ms) -90: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (1603 ms total) -90: -90: [----------] Global test environment tear-down -90: [==========] 14 tests from 2 test suites ran. (1725 ms total) -90: [ PASSED ] 14 tests. -90/96 Test #90: MdrunFEPTests ................................ Passed 1.92 sec -test 91 - Start 91: MdrunPullTests - -91: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunPullTests.xml" -91: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -91: Test timeout computed to be: 600 -91: [==========] Running 4 tests from 1 test suite. -91: [----------] Global test environment set-up. -91: [----------] 4 tests from PullTest/PullIntegrationTest -91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'r_1' has 3 atoms -91: Pull group 2 'r_2' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 1293.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: -91: NVE simulation: will use the initial temperature of 303.122 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 0.575 nm 0.600 nm -91: -91: There was 1 NOTE -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI process -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 20 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.058 0.029 199.7 -91: (ns/day) (hour/ns) -91: Performance: 61.948 0.387 -91: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (257 ms) -91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'r_1' has 3 atoms -91: Pull group 2 'r_2' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 1293.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: -91: NVE simulation: will use the initial temperature of 303.122 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 0.301 nm 0.400 nm -91: -91: There was 1 NOTE -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI process -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 20 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.033 0.017 199.4 -91: (ns/day) (hour/ns) -91: Performance: 108.797 0.221 -91: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (227 ms) -91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'r_1' has 3 atoms -91: Pull group 2 'r_2' has 3 atoms -91: Pull group 3 'r_3' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 1292.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: -91: NVE simulation: will use the initial temperature of 303.357 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 0.575 nm 0.500 nm -91: 1 3 2 -91: 3 3 8 0.331 nm 0.400 nm -91: -91: There was 1 NOTE -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI process -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 20 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.041 0.020 199.6 -91: (ns/day) (hour/ns) -91: Performance: 89.227 0.269 -91: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (235 ms) -91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 -91: Generating 1-4 interactions: fudge = 0.5 -91: Pull group 1 'r_1' has 3 atoms -91: Pull group 2 'r_2' has 3 atoms -91: Number of degrees of freedom in T-Coupling group System is 1293.00 -91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -91: -91: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: -91: NVE simulation: will use the initial temperature of 303.122 K for -91: determining the Verlet buffer size -91: -91: Pull group natoms pbc atom distance at start reference at t=0 -91: 1 3 2 -91: 2 3 5 0.575 nm 0.000 nm -91: 1 3 2 -91: 2 3 5 0.050 nm 0.000 nm -91: -91: There was 1 NOTE -91: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -91: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -91: Can not increase nstlist because an NVE ensemble is used -91: Using 1 MPI process -91: Using 2 OpenMP threads -91: -91: -91: NOTE: The number of threads is not equal to the number of (logical) cpus -91: and the -pin option is set to auto: will not pin threads to cpus. -91: This can lead to significant performance degradation. -91: Consider using -pin on (and -pinoffset in case you run multiple jobs). -91: starting mdrun 'spc2' -91: 20 steps, 0.0 ps. -91: Generated 330891 of the 330891 non-bonded parameter combinations -91: -91: Generated 330891 of the 330891 1-4 parameter combinations -91: -91: Excluding 2 bonded neighbours molecule type 'SOL' -91: -91: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/spc216.gro' -91: -91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K -91: -91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm -91: -91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm -91: -91: Note that mdrun will redetermine rlist based on the actual pair-list setup -91: -91: This run will generate roughly 0 Mb of data -91: -91: Writing final coordinates. -91: -91: Core t (s) Wall t (s) (%) -91: Time: 0.035 0.018 199.4 -91: (ns/day) (hour/ns) -91: Performance: 102.259 0.235 -91: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file -91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (233 ms) -91: [----------] 4 tests from PullTest/PullIntegrationTest (954 ms total) -91: -91: [----------] Global test environment tear-down -91: [==========] 4 tests from 1 test suite ran. (970 ms total) -91: [ PASSED ] 4 tests. -91/96 Test #91: MdrunPullTests ............................... Passed 1.16 sec -test 92 - Start 92: MdrunRotationTests - -92: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunRotationTests.xml" -92: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -92: Test timeout computed to be: 600 -92: [==========] Running 12 tests from 1 test suite. -92: [----------] Global test environment set-up. -92: [----------] 12 tests from RotationWorks/RotationTest -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 -92: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: trr version: GMX_trn_file (single precision) -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -207618084 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.025 0.012 199.1 -92: (ns/day) (hour/ns) -92: Performance: 362.158 0.066 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (19 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 -92: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 2130966732 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.017 0.009 198.7 -92: (ns/day) (hour/ns) -92: Performance: 527.671 0.045 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (14 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 -92: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -201859083 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.017 0.009 198.7 -92: (ns/day) (hour/ns) -92: Performance: 512.376 0.047 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (14 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 -92: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -38805521 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.024 0.012 199.1 -92: (ns/day) (hour/ns) -92: Performance: 365.651 0.066 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (18 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 -92: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 1005407103 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.027 0.013 199.0 -92: (ns/day) (hour/ns) -92: Performance: 333.643 0.072 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (20 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 -92: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 87031647 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.021 0.011 199.0 -92: (ns/day) (hour/ns) -92: Performance: 422.875 0.057 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (16 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 -92: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 2136959710 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.024 0.012 199.2 -92: (ns/day) (hour/ns) -92: Performance: 366.070 0.066 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (18 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 -92: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -704768294 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.017 0.008 198.8 -92: (ns/day) (hour/ns) -92: Performance: 535.970 0.045 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (14 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 -92: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 2107635702 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.021 0.010 199.0 -92: (ns/day) (hour/ns) -92: Performance: 433.090 0.055 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (16 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 -92: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -908599365 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.019 0.009 198.9 -92: (ns/day) (hour/ns) -92: Performance: 478.533 0.050 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (15 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 -92: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to -339904899 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.019 0.010 198.9 -92: (ns/day) (hour/ns) -92: Performance: 471.246 0.051 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (15 ms) -92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 -92: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 -92: -92: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -92: that with the Verlet scheme, nstlist has no effect on the accuracy of -92: your simulation. -92: -92: Rotation group 0 'system' has 4 atoms -92: Number of degrees of freedom in T-Coupling group rest is 9.00 -92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -92: -92: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: -92: NVE simulation with an initial temperature of zero: will use a Verlet -92: buffer of 10%. Check your energy drift! -92: -92: Enforced rotation: group 0 has 4 reference positions. -92: Reading them from /build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/rotref.0.trr. -92: -92: There were 2 NOTEs -92: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -92: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -92: Can not increase nstlist because an NVE ensemble is used -92: Using 1 MPI process -92: Using 2 OpenMP threads -92: -92: -92: NOTE: The number of threads is not equal to the number of (logical) cpus -92: and the -pin option is set to auto: will not pin threads to cpus. -92: This can lead to significant performance degradation. -92: Consider using -pin on (and -pinoffset in case you run multiple jobs). -92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' -92: 25 steps, 0.1 ps. -92: Setting the LD random seed to 786168249 -92: -92: Generated 1 of the 1 non-bonded parameter combinations -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonA' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonB' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonC' -92: -92: Excluding 1 bonded neighbours molecule type 'ArgonD' -92: -92: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero -92: -92: This run will generate roughly 0 Mb of data -92: -92: Writing final coordinates. -92: -92: Core t (s) Wall t (s) (%) -92: Time: 0.021 0.010 199.0 -92: (ns/day) (hour/ns) -92: Performance: 435.210 0.055 -92: Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file -92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 -92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (16 ms) -92: [----------] 12 tests from RotationWorks/RotationTest (201 ms total) -92: -92: [----------] Global test environment tear-down -92: [==========] 12 tests from 1 test suite ran. (224 ms total) -92: [ PASSED ] 12 tests. -92/96 Test #92: MdrunRotationTests ........................... Passed 0.42 sec -test 93 - Start 93: MdrunSimulatorComparison - -93: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" -93: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -93: Test timeout computed to be: 600 -93: [==========] Running 0 tests from 0 test suites. -93: [==========] 0 tests from 0 test suites ran. (0 ms total) -93: [ PASSED ] 0 tests. -93: -93: YOU HAVE 82 DISABLED TESTS -93: -93/96 Test #93: MdrunSimulatorComparison ..................... Passed 0.19 sec -test 94 - Start 94: MdrunVirtualSiteTests - -94: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.3/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.3/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" -94: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests -94: Test timeout computed to be: 600 -94: [==========] Running 37 tests from 2 test suites. -94: [----------] Global test environment set-up. -94: [----------] 1 test from VirtualSiteVelocityTest -94: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect -94: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) -94: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) -94: -94: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: -94: This run will generate roughly 0 Mb of data -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -94: NVE simulation with an initial temperature of zero: will use a Verlet -94: buffer of 10%. Check your energy drift! -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Can not increase nstlist because an NVE ensemble is used -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: -94: Dynamic load balancing report: -94: DLB was off during the run due to low measured imbalance. -94: Average load imbalance: 2.6%. -94: The balanceable part of the MD step is 41%, load imbalance is computed from this. -94: Part of the total run time spent waiting due to load imbalance: 1.1%. -94: -94: -94: NOTE: 46 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.022 0.011 198.3 -94: (ns/day) (hour/ns) -94: Performance: 71.403 0.336 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: trr version: GMX_trn_file (single precision) -94: -94: Reading virtual site types... -94: trr version: GMX_trn_file (single precision) -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -94: NVE simulation with an initial temperature of zero: will use a Verlet -94: buffer of 10%. Check your energy drift! -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Can not increase nstlist because an NVE ensemble is used -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: -94: Dynamic load balancing report: -94: DLB was off during the run due to low measured imbalance. -94: Average load imbalance: 3.3%. -94: The balanceable part of the MD step is 39%, load imbalance is computed from this. -94: Part of the total run time spent waiting due to load imbalance: 1.3%. -94: -94: -94: NOTE: 44 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.007 197.6 -94: (ns/day) (hour/ns) -94: Performance: 118.783 0.202 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (14 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -94: NVE simulation with an initial temperature of zero: will use a Verlet -94: buffer of 10%. Check your energy drift! -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Can not increase nstlist because an NVE ensemble is used -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: -94: Dynamic load balancing report: -94: DLB was off during the run due to low measured imbalance. -94: Average load imbalance: 5.2%. -94: The balanceable part of the MD step is 42%, load imbalance is computed from this. -94: Part of the total run time spent waiting due to load imbalance: 2.2%. -94: -94: -94: NOTE: 44 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.012 0.006 197.3 -94: (ns/day) (hour/ns) -94: Performance: 126.662 0.189 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (13 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 49 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.039 0.020 199.2 -94: (ns/day) (hour/ns) -94: Performance: 39.643 0.605 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (33 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 46 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.015 0.008 198.0 -94: (ns/day) (hour/ns) -94: Performance: 100.170 0.240 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (21 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.012 0.006 197.5 -94: (ns/day) (hour/ns) -94: Performance: 126.675 0.189 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -94: 1 -94: -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: Reading virtual site types... -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (19 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: Reading virtual site types... -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 5 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.006 197.5 -94: (ns/day) (hour/ns) -94: Performance: 121.392 0.198 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -94: 1 -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 5 NOTEs -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 47 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.019 0.010 198.4 -94: (ns/day) (hour/ns) -94: Performance: 79.910 0.300 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to -94: 1 -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (23 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: -94: NOTE 5 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 5 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.007 197.6 -94: (ns/day) (hour/ns) -94: Performance: 119.004 0.202 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -94: NVE simulation with an initial temperature of zero: will use a Verlet -94: buffer of 10%. Check your energy drift! -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Can not increase nstlist because an NVE ensemble is used -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: -94: Dynamic load balancing report: -94: DLB was off during the run due to low measured imbalance. -94: Average load imbalance: 2.9%. -94: The balanceable part of the MD step is 44%, load imbalance is computed from this. -94: Part of the total run time spent waiting due to load imbalance: 1.3%. -94: -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.014 0.007 197.6 -94: (ns/day) (hour/ns) -94: Performance: 111.649 0.215 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (14 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -94: NVE simulation with an initial temperature of zero: will use a Verlet -94: buffer of 10%. Check your energy drift! -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Can not increase nstlist because an NVE ensemble is used -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: -94: Dynamic load balancing report: -94: DLB was off during the run due to low measured imbalance. -94: Average load imbalance: 3.4%. -94: The balanceable part of the MD step is 45%, load imbalance is computed from this. -94: Part of the total run time spent waiting due to load imbalance: 1.6%. -94: -94: -94: NOTE: 44 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.012 0.006 197.5 -94: (ns/day) (hour/ns) -94: Performance: 126.324 0.190 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (13 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.014 0.007 197.6 -94: (ns/day) (hour/ns) -94: Performance: 112.950 0.212 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 46 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.016 0.008 198.1 -94: (ns/day) (hour/ns) -94: Performance: 96.675 0.248 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (22 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.014 0.007 197.5 -94: (ns/day) (hour/ns) -94: Performance: 112.895 0.213 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: ectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: Reading virtual site types... -94: -94: Reading virtual site types... -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.014 0.007 197.7 -94: (ns/day) (hour/ns) -94: Performance: 113.437 0.212 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (20 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 47 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.018 0.009 198.5 -94: (ns/day) (hour/ns) -94: Performance: 87.068 0.276 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (22 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.012 0.006 197.7 -94: (ns/day) (hour/ns) -94: Performance: 128.969 0.186 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (19 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Taking velocities from '/build/reproducible-path/gromacs-2025.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.006 197.8 -94: (ns/day) (hour/ns) -94: Performance: 122.952 0.195 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (19 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 46 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.006 197.6 -94: (ns/day) (hour/ns) -94: Performance: 122.774 0.195 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (24 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: -94: There were 4 NOTEs -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 46 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Core t (s) Wall t (s) (%) -94: Time: 0.013 0.007 197.9 -94: (ns/day) (hour/ns) -94: Performance: 114.651 0.209 -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: -94: Reading virtual site types... -94: Reading virtual site types... -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (25 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 -94: -94: NOTE 1 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note -94: that with the Verlet scheme, nstlist has no effect on the accuracy of -94: your simulation. -94: -94: -94: NOTE 2 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -94: Setting nstcalcenergy (100) equal to nstenergy (4) -94: -94: Number of degrees of freedom in T-Coupling group System is 45.00 -94: -94: NOTE 3 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -94: There are 6 non-linear virtual site constructions. Their contribution to -94: the energy error is approximated. In most cases this does not affect the -94: error significantly. -94: -94: -94: NOTE 4 [file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: -94: You are using a plain Coulomb cut-off, which might produce artifacts. -94: You might want to consider using PME electrostatics. -94: -94: -94: -94: There were 4 NOTEs -94: Generated 3 of the 6 non-bonded parameter combinations -94: -94: Excluding 3 bonded neighbours molecule type 'VSTEST' -94: -94: Cleaning up constraints and constant bonded interactions with virtual sites -94: -94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K -94: -94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm -94: -94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm -94: -94: Note that mdrun will redetermine rlist based on the actual pair-list setup -94: -94: This run will generate roughly 0 Mb of data -94: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 -94: -94: Update groups can not be used for this system because an incompatible virtual site type is used -94: -94: Using 2 MPI processes -94: Using 1 OpenMP thread per MPI process -94: -94: -94: NOTE: The number of threads is not equal to the number of (logical) cpus -94: and the -pin option is set to auto: will not pin threads to cpus. -94: This can lead to significant performance degradation. -94: Consider using -pin on (and -pinoffset in case you run multiple jobs). -94: starting mdrun 'Virtual sites test system in vacuo' -94: 8 steps, 0.0 ps. -94: -94: Writing final coordinates. -94: -94: NOTE: 45 % of the run time was spent communicating energies, -94: you might want to increase some nst* mdp options -94: -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Core t (s) Wall t (s) (%) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Time: 0.014 0.007 198.0 -94: (ns/day) (hour/ns) -94: Performance: 107.129 0.224 -94: Reading virtual site types... -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExp -94: ectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading file /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.3-Debian_2025.3_1 (single precision) -94: Reading virtual site types... -94: -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (26 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) -94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 -94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) -94: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (440 ms total) -94: -94: [----------] Global test environment tear-down -94: [==========] 37 tests from 2 test suites ran. (463 ms total) -94: [ PASSED ] 37 tests. -94/96 Test #94: MdrunVirtualSiteTests ........................ Passed 0.73 sec -test 95 - Start 95: EnsembleHistogramPotentialPlugin.ForceCalc - -95: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" -95: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests -95: Test timeout computed to be: 1500 -95: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc -95: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc -95: [==========] Running 1 test from 1 test suite. -95: [----------] Global test environment set-up. -95: [----------] 1 test from EnsembleHistogramPotentialPlugin -95: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc -95: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) -95: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) -95: -95: [----------] Global test environment tear-down -95: [==========] 1 test from 1 test suite ran. (0 ms total) -95: [ PASSED ] 1 test. -95/96 Test #95: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.16 sec -test 96 - Start 96: EnsembleBoundingPotentialPlugin.ForceCalc - -96: Test command: /build/reproducible-path/gromacs-2025.3/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" -96: Working Directory: /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/tests -96: Test timeout computed to be: 1500 -96: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc -96: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc -96: [==========] Running 1 test from 1 test suite. -96: [----------] Global test environment set-up. -96: [----------] 1 test from EnsembleBoundingPotentialPlugin -96: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc -96: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) -96: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) -96: -96: [----------] Global test environment tear-down -96: [==========] 1 test from 1 test suite ran. (0 ms total) -96: [ PASSED ] 1 test. -96/96 Test #96: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.16 sec - -100% tests passed, 0 tests failed out of 96 - -Label Time Summary: -GTest = 264.75 sec*proc (92 tests) -IntegrationTest = 162.05 sec*proc (31 tests) -MpiTest = 155.85 sec*proc (23 tests) -QuickGpuTest = 57.41 sec*proc (23 tests) -SlowGpuTest = 139.25 sec*proc (14 tests) -SlowTest = 86.96 sec*proc (14 tests) -UnitTest = 15.74 sec*proc (47 tests) - -Total Test time (real) = 144.51 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ @@ -335841,10 +7909,10 @@ -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex --- Configuring done (25.3s) --- Generating done (1.0s) +-- Configuring done (30.0s) +-- Generating done (1.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.3/build/documentation -/usr/bin/make -j40 manual -C build/documentation +/usr/bin/make -j42 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 @@ -335860,38 +7928,38 @@ /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory 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/build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -335904,87 +7972,89 @@ make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/parser.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/sgangle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/sgangle.png -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection && 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/scanner.cpp +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/decomp.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/decomp.png -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr/xdr.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g 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src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/lmfit/lmmin.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -MF CMakeFiles/muparser.dir/src/muParserDLL.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/muparser/src/muParserDLL.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserError.cpp.o -MF CMakeFiles/muparser.dir/src/muParserError.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserError.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/muparser/src/muParserError.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/gmx.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvar.cpp +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/mdrun/mdrun.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/compress.c: In function 'compress2': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/compress.c:22:14: warning: old-style function definition [-Wold-style-definition] @@ -336014,38 +8084,6 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/adler32.c:200:15: warning: old-style function definition [-Wold-style-definition] 200 | uLong ZEXPORT adler32_combine64(adler1, adler2, len2) uLong adler1; | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:214:23: warning: old-style function definition [-Wold-style-definition] - 214 | unsigned long ZEXPORT crc32(crc, buf, len) unsigned long crc; - | ^~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_little': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:275:21: warning: old-style function definition [-Wold-style-definition] - 275 | local unsigned long crc32_little(crc, buf, len) unsigned long crc; - | ^~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_big': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:328:21: warning: old-style function definition [-Wold-style-definition] - 328 | local unsigned long crc32_big(crc, buf, len) unsigned long crc; - | ^~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'gf2_matrix_times': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:372:21: warning: old-style function definition [-Wold-style-definition] - 372 | local unsigned long gf2_matrix_times(mat, vec) unsigned long* mat; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'gf2_matrix_square': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:389:16: warning: old-style function definition [-Wold-style-definition] - 389 | local void gf2_matrix_square(square, mat) unsigned long* square; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine_': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:399:13: warning: old-style function definition [-Wold-style-definition] - 399 | local uLong crc32_combine_(crc1, crc2, len2) uLong crc1; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:456:15: warning: old-style function definition [-Wold-style-definition] - 456 | uLong ZEXPORT crc32_combine(crc1, crc2, len2) uLong crc1; - | ^~~~~~~~~~~~~ -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine64': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:463:15: warning: old-style function definition [-Wold-style-definition] - 463 | uLong ZEXPORT crc32_combine64(crc1, crc2, len2) uLong crc1; - | ^~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c: In function 'deflateInit_': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:205:13: warning: old-style function definition [-Wold-style-definition] 205 | int ZEXPORT deflateInit_(strm, level, version, stream_size) z_streamp strm; @@ -336090,7 +8128,6 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:584:15: warning: old-style function definition [-Wold-style-definition] 584 | uLong ZEXPORT deflateBound(strm, sourceLen) z_streamp strm; | ^~~~~~~~~~~~ -[ 0%] Built target release-version-info /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c: In function 'putShortMSB': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:642:12: warning: old-style function definition [-Wold-style-definition] 642 | local void putShortMSB(s, b) deflate_state* s; @@ -336103,7 +8140,6 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:680:13: warning: old-style function definition [-Wold-style-definition] 680 | int ZEXPORT deflate(strm, flush) z_streamp strm; | ^~~~~~~ -cd /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -MF CMakeFiles/muparser.dir/src/muParserCallback.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/muparser/src/muParserCallback.cpp /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c: In function 'deflateEnd': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:1026:13: warning: old-style function definition [-Wold-style-definition] 1026 | int ZEXPORT deflateEnd(strm) z_streamp strm; @@ -336144,51 +8180,72 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:1958:19: warning: old-style function definition [-Wold-style-definition] 1958 | local block_state deflate_rle(s, flush) deflate_state* s; | ^~~~~~~~~~~ -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/alltoall.cpp /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c: In function 'deflate_huff': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/deflate.c:2040:19: warning: old-style function definition [-Wold-style-definition] 2040 | local block_state deflate_huff(s, flush) deflate_state* s; | ^~~~~~~~~~~~ +[ 0%] Built target release-version-info +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/programs/legacymodules.cpp +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c: In function 'inflate_fast': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c:67:20: warning: old-style function definition [-Wold-style-definition] + 67 | void ZLIB_INTERNAL inflate_fast(strm, start) z_streamp strm; + | ^~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:214:23: warning: old-style function definition [-Wold-style-definition] + 214 | unsigned long ZEXPORT crc32(crc, buf, len) unsigned long crc; + | ^~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_little': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:275:21: warning: old-style function definition [-Wold-style-definition] + 275 | local unsigned long crc32_little(crc, buf, len) unsigned long crc; + | ^~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_big': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:328:21: warning: old-style function definition [-Wold-style-definition] + 328 | local unsigned long crc32_big(crc, buf, len) unsigned long crc; + | ^~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'gf2_matrix_times': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:372:21: warning: old-style function definition [-Wold-style-definition] + 372 | local unsigned long gf2_matrix_times(mat, vec) unsigned long* mat; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'gf2_matrix_square': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:389:16: warning: old-style function definition [-Wold-style-definition] + 389 | local void gf2_matrix_square(square, mat) unsigned long* square; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine_': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:399:13: warning: old-style function definition [-Wold-style-definition] + 399 | local uLong crc32_combine_(crc1, crc2, len2) uLong crc1; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:456:15: warning: old-style function definition [-Wold-style-definition] + 456 | uLong ZEXPORT crc32_combine(crc1, crc2, len2) uLong crc1; + | ^~~~~~~~~~~~~ +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c: In function 'crc32_combine64': +/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/crc32.c:463:15: warning: old-style function definition [-Wold-style-definition] + 463 | uLong ZEXPORT crc32_combine64(crc1, crc2, len2) uLong crc1; + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/int-mat.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/int-mat.png +cd 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-I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/options.cpp -[ 0%] Built target internal_rpc_xdr -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT 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/build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/ring.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/ring.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c: In function 'inflate_fast': -/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inffast.c:67:20: warning: old-style function definition [-Wold-style-definition] - 67 | void ZLIB_INTERNAL inflate_fast(strm, start) z_streamp strm; - | ^~~~~~~~~~~~ -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/shiftf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/shiftf.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT 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-D GMX_GCC_MINIMUM_REQUIRED_VERSION=11 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2025.3/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2025.3 -D GMX_CUDA_MINIMUM_REQUIRED_COMPUTE_CAPABILITY=5.0 -D GMX_CUDA_MINIMUM_REQUIRED_VERSION=12.1 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2025.3/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Brian Andrews, Vladimir Basov, Paul Bauer, Hugh Bird, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Petter Johansson, Carsten Kutzner, Grzegorz Łazarski, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Lukas Müllender, Julien Nabet, Szilárd Páll, Andrea Pasquadibisceglie, Michele Pellegrino, Nicola Piasentin, Daniele Rapetti, Muhammad Umair Sadiq, Hubert Santuz, Roland Schulz, Michael Shirts, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermühle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Cathrine Bergh, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2025.3/cmake/gmxConfigureVersionInfo.cmake +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/parsort.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/parsort.png /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c: In function 'inflateResetKeep': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c:102:13: warning: old-style function definition [-Wold-style-definition] 102 | int ZEXPORT inflateResetKeep(strm) z_streamp strm; @@ -336225,6 +8282,7 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c:634:13: warning: old-style function definition [-Wold-style-definition] 634 | int ZEXPORT inflate(strm, flush) z_streamp strm; | ^~~~~~~ +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/conf.py /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c: In function 'inflateEnd': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c:1361:13: warning: old-style function definition [-Wold-style-definition] 1361 | int ZEXPORT inflateEnd(strm) z_streamp strm; @@ -336265,70 +8323,76 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inflate.c:1618:14: warning: old-style function definition [-Wold-style-definition] 1618 | long ZEXPORT inflateMark(strm) z_streamp strm; | ^~~~~~~~~~~ -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/dd-cells.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-cells.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/p2p_send_recv.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsassigner.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/options/optionsection.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inftrees.c -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/mtf.c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inftrees.c: In function 'inflate_table': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/inftrees.c:31:19: warning: old-style function definition [-Wold-style-definition] 31 | int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work) codetype type; | ^~~~~~~~~~~~~ -/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/dd-tric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-tric.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/bcast.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.28 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2025.3/admin -D GMX_CLANG_MINIMUM_REQUIRED_VERSION=14 -D GMX_GCC_MINIMUM_REQUIRED_VERSION=11 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2025.3/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2025.3 -D GMX_CUDA_MINIMUM_REQUIRED_COMPUTE_CAPABILITY=5.0 -D GMX_CUDA_MINIMUM_REQUIRED_VERSION=12.1 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2025.3/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Brian Andrews, Vladimir Basov, Paul Bauer, Hugh Bird, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Petter Johansson, Carsten Kutzner, Grzegorz Łazarski, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Lukas Müllender, Julien Nabet, Szilárd Páll, Andrea Pasquadibisceglie, Michele Pellegrino, Nicola Piasentin, Daniele Rapetti, Muhammad Umair Sadiq, Hubert Santuz, Roland Schulz, Michael Shirts, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermühle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Cathrine Bergh, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2025.3/cmake/gmxConfigureVersionInfo.cmake -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/conf.py +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/ring.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/ring.png cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/index.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/index.rst +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +[ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/texindex.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/download.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/download.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvaratoms.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/plots/shiftf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/plots/shiftf.png +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -g -O2 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-I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/rle.c -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/p2p_wait.cpp -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/tng_compress.c +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst -[ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/free2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free2.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/leapfrog.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/leapfrog.png cd 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-pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-tric.png cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/index.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/profile.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/comm.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/lz77.c +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/flowchart.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/flowchart.png +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/language-features.rst +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/naming.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_alb.cpp +[ 0%] Built target gmx_objlib +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram.cpp +[ 0%] Built target lmfit_objlib +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/overview.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/trees.c +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/algorithms/plots/free1.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free1.png +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.3/src/external/tng_io/src/compression/merge_sort.c +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/trees.c: In function '_tr_init': /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/trees.c:399:20: warning: old-style function definition [-Wold-style-definition] 399 | void ZLIB_INTERNAL _tr_init(s) deflate_state* s; @@ -336413,49 +8477,24 @@ /build/reproducible-path/gromacs-2025.3/src/external/tng_io/external/zlib/trees.c:1295:12: warning: old-style function definition [-Wold-style-definition] 1295 | local void copy_block(s, buf, len, header) deflate_state* s; | ^~~~~~~~~~ -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_combination.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/language-features.rst -[ 0%] Built target energyanalysis -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/naming.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/profile.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/comm.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/colvars/colvarcomp_coordnums.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/overview.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd 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/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/src/numa_malloc.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g 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/build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/phipsi.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/phipsi.png -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rama.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rama.png cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/user-guide/force-fields.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/user-guide/force-fields.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rdfO-O.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdfO-O.png cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/user-guide/getting-started.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/user-guide/getting-started.rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rdf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdf.png cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/user-guide/index.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/user-guide/index.rst cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/user-guide/known-issues.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/user-guide/known-issues.rst cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/user-guide/managing-simulations.rst /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/user-guide/managing-simulations.rst @@ -336885,12 +8953,12 @@ cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rama.pdf /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rama.pdf cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rdfO-O.pdf /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdfO-O.pdf cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.3/docs/reference-manual/analysis/plots/rdf.pdf /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdf.pdf +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-image-conversion-timestamp.txt cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 28%] Built target sphinx-input-rst -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-image-conversion-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 34%] Built target sphinx-image-conversion +[ 16%] Built target sphinx-image-conversion +[ 34%] Built target sphinx-input-rst cd /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,--dependency-file=CMakeFiles/muparser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so @@ -336921,26 +8989,26 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidegpuusage.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp -cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/findallgputasks.cpp +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/energydata.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/expandedensembleelement.cpp +cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.3/src/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.3/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.3/src -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.3/src/external -isystem /build/reproducible-path/gromacs-2025.3/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp @@ -337795,8 +9863,8 @@ cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -337870,9 +9938,9 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual && /usr/bin/sphinx-build -q -b latex -w sphinx-latex.log -d /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual/_latex_doctrees -t do_latex /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.3/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ [ref.any] @@ -373497,7 +45565,7 @@ ts/type1/urw/times/utmbi8a.pfb> -Output written on gromacs.pdf (835 pages, 13193211 bytes). +Output written on gromacs.pdf (835 pages, 13193213 bytes). Transcript written on gromacs.log. cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) @@ -375871,7 +47939,7 @@ ts/type1/urw/times/utmbi8a.pfb> -Output written on gromacs.pdf (843 pages, 13624957 bytes). +Output written on gromacs.pdf (843 pages, 13624944 bytes). Transcript written on gromacs.log. cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2025.3/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) @@ -378240,7 +50308,7 @@ ts/type1/urw/times/utmbi8a.pfb> -Output written on gromacs.pdf (843 pages, 13624965 bytes). +Output written on gromacs.pdf (843 pages, 13624951 bytes). Transcript written on gromacs.log. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' [100%] Built target pdf @@ -378257,7 +50325,7 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -j40 man -C build/documentation +/usr/bin/make -j42 man -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 @@ -378277,10 +50345,10 @@ cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" @@ -378297,9 +50365,9 @@ cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/muparser /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -378314,8 +50382,8 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake @@ -378325,102 +50393,102 @@ [ 5%] Built target sphinx-image-conversion make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' [ 5%] Built target release-version-info +/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build -/usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build -make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +[ 7%] Built target internal_rpc_xdr +[ 31%] Built target sphinx-input-rst make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. +make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" -[ 8%] Built target tng_io_zlib -[ 8%] Built target lmfit_objlib -[ 8%] Built target scanner -[ 8%] Built target linearalgebra -[ 8%] Built target internal_rpc_xdr -[ 8%] Built target tng_io_obj -[ 8%] Built target energyanalysis -[ 10%] Built target thread_mpi -[ 11%] Built target muparser -[ 11%] Built target gmx_objlib -[ 11%] Built target mdrun_objlib +[ 37%] Built target muparser +[ 37%] Built target tng_io_obj +[ 37%] Built target linearalgebra +[ 37%] Built target scanner +[ 37%] Built target colvars_objlib +[ 38%] Built target tng_io_zlib +[ 38%] Built target lmfit_objlib +[ 41%] Built target thread_mpi +[ 41%] Built target options +[ 41%] Built target energyanalysis +[ 41%] Built target gmx_objlib +[ 41%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend -[ 13%] Built target options make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 38%] Built target sphinx-input-rst -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 38%] Built target pulling -[ 41%] Built target colvars_objlib +[ 41%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -378455,9 +50523,9 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -378501,9 +50569,9 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2025.3/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.3/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.3/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -378512,7 +50580,7 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -j40 webpage -C build/documentation +/usr/bin/make -j42 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 @@ -378529,177 +50597,181 @@ /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/muparser /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.3/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs /build/reproducible-path/gromacs-2025.3/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs 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PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-image-conversion.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make 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-/usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory 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src/gromacs/options/CMakeFiles/options.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +/usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/doxygen-source-timestamp.txt make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. +make[4]: Nothing to be done for 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'src/gromacs/options/CMakeFiles/options.dir/build'. +make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build -[ 8%] Built target tng_io_obj -[ 8%] Built target muparser -[ 8%] Built target lmfit_objlib -[ 10%] Built target tng_io_zlib -[ 10%] Built target scanner -[ 10%] Built target linearalgebra -/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend +[ 0%] Built target lmfit_objlib +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 10%] Built target mdrun_objlib -[ 10%] Built target energyanalysis -[ 11%] Built target options +[ 0%] Built target scanner +[ 11%] Built target muparser [ 13%] Built target thread_mpi +[ 2%] Built target energyanalysis +[ 2%] Built target linearalgebra +[ 13%] Built target tng_io_zlib +[ 13%] Built target tng_io_obj +[ 13%] Built target sphinx-image-conversion +[ 2%] Built target internal_rpc_xdr +[ 2%] Built target gmx_objlib +[ 2%] Built target mdrun_objlib +[ 13%] Built target options +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" -[ 13%] Built target gmx_objlib -[ 13%] Built target release-version-info +[ 16%] Built target colvars_objlib +[ 16%] Built target doxygen-source-timestamp +[ 16%] Built target release-version-info /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs /build/reproducible-path/gromacs-2025.3/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" -[ 13%] Built target doxygen-source-timestamp +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -/usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build -[ 16%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.3/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2025.3/cmake/gmxConfigureVersionInfo.cmake -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +[ 16%] Built target pulling make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -[ 16%] Built target pulling +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" -[ 41%] Built target sphinx-input-rst make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +[ 17%] Built target doxygen-version +[ 41%] Built target sphinx-input-rst +/usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' @@ -378707,21 +50779,17 @@ make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build -[ 41%] Built target doxygen-version -/usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" -[ 41%] Built target taskassignment -make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/depgraphs +make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +[ 41%] Built target taskassignment +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake [ 42%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. @@ -378807,9 +50875,9 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2025.3/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2025.3/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.3/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) +intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.3/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: @@ -378844,18 +50912,18 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command @@ -379070,22 +51138,22 @@ make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' +/usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/depgraphs -/usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2025.3/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2025.3 -B /build/reproducible-path/gromacs-2025.3/build/documentation -o /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... -warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. - To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" /build/reproducible-path/gromacs-2025.3/docs/doxygen/doxygenxml.py:58: SyntaxWarning: invalid escape sequence '\l' contents of the detailed description (presence of a \libinternal command in /build/reproducible-path/gromacs-2025.3/docs/doxygen/doxygenxml.py:343: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2025.3/docs/doxygen/doxygenxml.py:350: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" +warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. + To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Scanning source tree... Reading source files... Reading Doxygen XML files... @@ -379100,18 +51168,18 @@ make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' -make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build +make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/depgraphs make[4]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/documentation' cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen/depgraphs -cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake -NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but veryNOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. likely produce extra warnings. - +cd /build/reproducible-path/gromacs-2025.3/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake +NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... +NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" @@ -379119,8 +51187,6 @@ To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed -libpath/shortest.c:324: triangulation failed -libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file @@ -379142,11 +51208,11 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command -/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command +/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. @@ -379967,6 +52033,8 @@ [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed +libpath/shortest.c:324: triangulation failed +libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.3/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file @@ -379988,17 +52056,17 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command -/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command -/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command +/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved @@ -381242,20 +53310,20 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command -/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command -/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found +/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command +/build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found -/build/reproducible-path/gromacs-2025.3/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command +/build/reproducible-path/gromacs-2025.3/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.3/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved @@ -381420,18 +53488,14 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. @@ -381440,6 +53504,10 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. @@ -381512,11 +53580,11 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:611: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:622: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:138: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. @@ -381538,32 +53606,32 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/pairs.cpp:173: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/pairs.cpp:173: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/tests/constrtestrunners.h:63: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. @@ -381612,13 +53680,13 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. @@ -381952,6 +54020,10 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:198: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:130: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:143: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. @@ -381962,10 +54034,6 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:204: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:205: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/atoms.cpp:206: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/topology/symtab.cpp:332: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. @@ -382000,6 +54068,15 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. +/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. @@ -382014,15 +54091,6 @@ /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. -/build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.3/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. @@ -383702,7 +55770,7 @@ dh_testroot dh_prep dh_installdirs -/usr/bin/make -j40 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp +/usr/bin/make -j42 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 @@ -383710,72 +55778,81 @@ /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend -/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi 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directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs 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src/gromacs/CMakeFiles/colvars_objlib.dir/build +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' @@ -383784,44 +55861,35 @@ make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. +make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 0%] Built target internal_rpc_xdr -[ 0%] Built target lmfit_objlib -[ 2%] Built target thread_mpi -[ 2%] Built target scanner +[ 0%] Built target scanner +[ 2%] Built target lmfit_objlib +[ 2%] Built target linearalgebra +[ 4%] Built target thread_mpi [ 4%] Built target tng_io_obj -[ 4%] Built target linearalgebra -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 6%] Built target gmx_objlib +[ 4%] Built target energyanalysis /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend -[ 6%] Built target energyanalysis -[ 6%] Built target mdrun_objlib -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" +[ 4%] Built target mdrun_objlib +[ 6%] Built target gmx_objlib [ 8%] Built target options make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 8%] Built target release-version-info +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" +[ 13%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build -[ 13%] Built target colvars_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' @@ -383833,16 +55901,16 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build +/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build -[ 13%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +[ 13%] Built target taskassignment [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' @@ -383857,33 +55925,33 @@ /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.3/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +[ 97%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build +/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -[ 97%] Built target gmx [ 97%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend @@ -383898,8 +55966,8 @@ make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. @@ -383911,19 +55979,19 @@ /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" -[100%] Built target argon-forces-integration -[100%] Built target methane-water-integration +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +cd /build/reproducible-path/gromacs-2025.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.3/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +[100%] Built target argon-forces-integration +[100%] Built target methane-water-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' +/usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. @@ -383955,452 +56023,452 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atom_nom.tbl --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.gro --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-8.xvg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/elements.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ps.m2p --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-10.xvg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/elements.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdw-msms.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/electroneg.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-8.xvg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.gro +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-10.xvg +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.zsh @@ -384415,55 +56483,55 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session/resources.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdsignals.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/tpr.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/basicdefinitions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/util.hpp +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/setup.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/integrator.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/vector.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/simulationstate.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi.so.10 @@ -384479,110 +56547,110 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion-gmx_mpi.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hydorder.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tcaf.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsf.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densmap.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-h2order.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-confrms.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helix.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdrun.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdmat.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-x2top.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-potential.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-distance.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dielectric.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-scattering.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi' -/usr/bin/make -j40 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp +/usr/bin/make -j42 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.3/build/mpi-dp//CMakeFiles/progress.marks @@ -384592,35 +56660,35 @@ /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" @@ -384629,40 +56697,31 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.3/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.3-1 -P /build/reproducible-path/gromacs-2025.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 0%] Built target release-version-info +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. +/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. @@ -384674,54 +56733,63 @@ make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. +make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' [ 0%] Built target lmfit_objlib -[ 0%] Built target internal_rpc_xdr -[ 0%] Built target tng_io_obj +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' [ 0%] Built target thread_mpi -[ 0%] Built target linearalgebra +[ 0%] Built target internal_rpc_xdr [ 0%] Built target scanner +[ 0%] Built target linearalgebra [ 0%] Built target energyanalysis -[ 0%] Built target mdrun_objlib -[ 0%] Built target gmx_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend +[ 0%] Built target tng_io_obj +[ 0%] Built target gmx_objlib +[ 0%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" +[ 0%] Built target release-version-info [ 0%] Built target options -[ 4%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 4%] Built target pulling +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +[ 0%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.3/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi-dp /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" +[ 4%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +[ 4%] Built target taskassignment +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 4%] Built target taskassignment [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' @@ -384746,18 +56814,18 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +[ 95%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build -[ 95%] Built target gmx +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -[ 97%] Built target gmxapi -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' +[ 97%] Built target gmxapi [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend @@ -384789,452 +56857,452 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: 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--- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/elements.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdw-msms.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/electroneg.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-8.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-10.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.zsh @@ -385249,55 +57317,55 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session/resources.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdsignals.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/basicdefinitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/util.hpp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/setup.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/vector.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/simulationstate.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.10 @@ -385313,110 +57381,110 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hydorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tcaf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densmap.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-h2order.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hydorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-confrms.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tcaf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helix.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdrun.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densmap.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-h2order.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-confrms.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helix.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdrun.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdmat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-x2top.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-potential.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-distance.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dielectric.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-scattering.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/mpi-dp' -/usr/bin/make -j40 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp +/usr/bin/make -j42 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2025.3/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.3 -B/build/reproducible-path/gromacs-2025.3/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.3/build/basic//CMakeFiles/progress.marks @@ -385425,137 +57493,137 @@ /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic 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src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs 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+/usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" +cd 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src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/energyanalysis 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'/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build +/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. +cd /build/reproducible-path/gromacs-2025.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.3-Debian_2025.3_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.3/build/basic/VersionInfo-partial.cmake.cmakein -D 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'/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. +make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +[ 0%] Built target lmfit_objlib [ 0%] Built target internal_rpc_xdr make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [ 0%] Built target scanner +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 0%] Built target linearalgebra [ 0%] Built target energyanalysis -/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build [ 2%] Built target tng_io_obj -[ 2%] Built target linearalgebra -[ 6%] Built target thread_mpi -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 2%] Built target gmx_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend +[ 2%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. -make[3]: Leaving directory 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directory '/build/reproducible-path/gromacs-2025.3/build/basic' +/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -[ 12%] Built target pulling +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' +[ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" +[ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Nothing to be done for 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share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/share/template /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/share/template /build/reproducible-path/gromacs-2025.3/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' 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'/build/reproducible-path/gromacs-2025.3/build/basic' +cd /build/reproducible-path/gromacs-2025.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic /build/reproducible-path/gromacs-2025.3/build/basic/src/programs /build/reproducible-path/gromacs-2025.3/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build +/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory 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'/build/reproducible-path/gromacs-2025.3/build/basic' @@ -385601,25 +57681,13 @@ /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build -[ 97%] Built target argon-forces-integration -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic' -make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. +make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' [100%] Built target methane-water-integration -[100%] Built target template -[100%] Built target gmx +[100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall @@ -385637,452 +57705,452 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: 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/build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ps.m2p --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-10.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/elements.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdw-msms.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/electroneg.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-8.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-10.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp +-- Up-to-date: 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/build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.zsh @@ -386090,100 +58158,100 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionenums.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selection.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/nbsearch.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/indexutil.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/position.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectioncollection.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoption.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectory --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/restraint --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/confio.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/filetypes.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/trxio.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/pdbio.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/oenv.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/tpxio.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/idef.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/topology_enums.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/index.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/atomprop.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/symtab.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/block.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/ifunc.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/atoms.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/topology.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/gmxassert.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/flags.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/pleasecite.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/listoflists.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/exceptions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/classhelpers.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/stringutil.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/real.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/futil.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/smalloc.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/range.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/classhelpers.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/unique_cptr.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/gmxassert.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/arrayref.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/baseversion.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/range.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/programcontext.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/basedefinitions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/fileptr.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/current_function.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/programcontext.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/utility/futil.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectory +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/index.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/topology.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/ifunc.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/topology_enums.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/atoms.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/symtab.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/block.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/idef.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/topology/atomprop.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/restraint +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/optionflags.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/options.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/basicoptions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/filenameoption.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/optionfiletype.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/abstractoption.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/ivaluestore.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/pbcutil --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/pbcutil/pbc.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/do_fit.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/vectypes.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/utilities.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/functions.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/vec.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/units.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/filenameoption.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/lifetime.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/plot.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h --- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/vectypes.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/do_fit.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/utilities.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/vec.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/functions.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/math/units.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/pbcutil +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/pbcutil/pbc.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectioncollection.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/indexutil.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/nbsearch.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoption.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selection.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionenums.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/selection/position.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/oenv.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/filetypes.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/trxio.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/confio.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/tpxio.h +-- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so.0.4.0 @@ -386194,55 +58262,55 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session/resources.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdsignals.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/basicdefinitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/util.hpp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/setup.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/vector.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/simulationstate.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h @@ -386260,110 +58328,110 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hydorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tcaf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densmap.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-h2order.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-confrms.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helix.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdrun.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-x2top.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" +/usr/bin/make -f 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"--color=" +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp 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/build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs /build/reproducible-path/gromacs-2025.3/build/basic-dp 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src/gromacs/CMakeFiles/lmfit_objlib.dir/build +/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. +/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. +make[3]: Nothing to be done for 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'/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build -/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build -[ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. +/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build +[ 0%] Built target lmfit_objlib [ 0%] Built target internal_rpc_xdr +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 0%] Built target linearalgebra +[ 0%] Built target scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 0%] Built target lmfit_objlib -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 2%] Built target tng_io_obj -[ 2%] Built target energyanalysis -/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build +[ 0%] Built target linearalgebra +[ 0%] Built target energyanalysis +[ 0%] Built target gmx_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend -[ 6%] Built target thread_mpi -[ 8%] Built target release-version-info -[ 8%] Built target gmx_objlib +[ 0%] Built target mdrun_objlib +[ 2%] Built target tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" -[ 8%] Built target mdrun_objlib +[ 4%] Built target release-version-info +[ 8%] Built target thread_mpi [ 8%] Built target options -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build -[ 12%] Built target colvars_objlib +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 14%] Built target pulling +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +[ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build +[ 14%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +[ 14%] Built target taskassignment +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 14%] Built target taskassignment [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' @@ -386517,29 +58585,29 @@ /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.3/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build +[ 95%] Built target gmx make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 95%] Built target gmx +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' +/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[ 97%] Built target nblib -[100%] Built target gmxapi +[ 97%] Built target gmxapi +[100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' @@ -386547,8 +58615,8 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' cd /build/reproducible-path/gromacs-2025.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.3 /build/reproducible-path/gromacs-2025.3/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic-dp /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.3/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build +make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. @@ -386556,8 +58624,8 @@ make[3]: Entering directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' -[100%] Built target argon-forces-integration [100%] Built target methane-water-integration +[100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.3/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall @@ -386570,452 +58638,452 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/nsfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b +-- Up-to-date: 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/build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sfactor.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a5.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/elements.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/edissoc.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/co-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdw-msms.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/random.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG53a6.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/electroneg.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/defselection.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/atommass.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ss.map +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/vdwradii.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-8.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc216.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/bonds.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.dtd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/export.dlg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/xlateat.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residues.xml +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-11.xvg +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip5p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.gro +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/dgsolv.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/cb-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexspc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp --- Up-to-date: 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/build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/residuetypes.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a1.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/surface.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/README +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp +-- Up-to-date: 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/build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/phbres.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/refi_aa.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/tip3p.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG43a2.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ffG45a3.itp --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/ca-shift.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/GMXRC.zsh @@ -387030,55 +59098,55 @@ -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session/resources.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/context.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/session.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/md/mdsignals.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapi.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gmxapicompat.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/status.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/compat/mdparams.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/gromacsfwd.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/tpr.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/basicdefinitions.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/util.hpp +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/util/setup.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particletype.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/vector.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/topology.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/calculator.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/definitions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/simulationstate.h --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/interactions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/nblib.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/kerneloptions.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/particlesequencer.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/exception.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/molecules.h +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.10 @@ -387094,108 +59162,108 @@ -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hydorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tcaf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spol.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dipoles.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-clustsize.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densmap.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-h2order.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-densorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-analyze.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-check.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-wheel.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-confrms.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saltbr.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helix.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-spatial.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-anaeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdrun.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-editconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pairdist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genconf.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-current.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-angle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-grompp.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-solvate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sasa.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-vanhove.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mdmat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dos.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-eneconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-polystat.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bundle.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-select.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmens.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-helixorient.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjorder.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gangle.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rms.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-x2top.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-density.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmeig.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-bar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dump.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-gyrate.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjconv.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-disre.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-chi.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sigeps.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-report-methods.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-help.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trjcat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-potential.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-covar.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-trajectory.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-traj.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-enemat.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-velacc.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-distance.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-mindist.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-dielectric.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-filter.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-make_edi.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-freevolume.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-cluster.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-order.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-msd.1 +-- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-scattering.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-awh.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-rotacf.1 --- Up-to-date: /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.3/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2025.3/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* @@ -387223,7 +59291,7 @@ Now scanning "/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc", found 24753 files. Now have 24753 files in total. Removed 0 files due to nonunique device and inode. -Total size is 413701956 bytes or 395 MiB +Total size is 413714545 bytes or 395 MiB Removed 8205 files due to unique sizes from list. 16548 files left. Now eliminating candidates based on first bytes: removed 3539 files from list. 13009 files left. Now eliminating candidates based on last bytes: removed 1801 files from list. 11208 files left. @@ -387234,8814 +59302,8814 @@ Now making symbolic links. creating Making 4404 links. symlinks -r -s -c /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/ -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classEwaldBoxZScaler-members.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler-members.xhtml -> ../html-full/classEwaldBoxZScaler-members.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -> ../html-full/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -> ../html-full/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setenv_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setenv_8h__incl.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setenv_8h__incl.svg -> ../html-full/setenv_8h__incl.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__ilist.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist.xhtml -> ../html-full/structt__ilist.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_148.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_306.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_148.svg -> ../html-full/inherit_graph_306.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator__impl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/alignedallocator__impl_8h__incl.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator__impl_8h__incl.svg -> ../html-full/alignedallocator__impl_8h__incl.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/valuestore_8h__incl.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/requirements_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/requirements_8h__incl.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/requirements_8h__incl.svg -> ../html-full/requirements_8h__incl.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_2.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_2.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_2.js -> ../../html-full/search/groups_2.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1d.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> all_1d.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1a.js -> all_1c.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_5.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> ../../html-full/search/groups_5.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_b.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> ../../html-full/search/groups_b.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_7.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> ../../html-full/search/pages_7.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_1.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> ../../html-full/search/groups_1.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_a.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> ../../html-full/search/groups_a.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_15.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> ../../html-full/search/enums_15.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/close.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> ../../html-full/search/close.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_c.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> ../../html-full/search/pages_c.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_14.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_14.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_14.js -> ../../html-full/search/enums_14.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_8.js -> 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-changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> ../../html-full/search/groups_10.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_c.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> ../../html-full/search/groups_c.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> ../../html-full/search/groups_3.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_d.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_f.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_d.js -> ../../html-full/search/related_f.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_9.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> ../../html-full/search/groups_9.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_7.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_7.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_7.js -> ../../html-full/search/groups_7.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_0.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> ../../html-full/search/pages_0.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> 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-changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_d.js -> ../../html-full/search/pages_e.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> ../../html-full/search/search.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_8.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> ../../html-full/search/related_8.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_12.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> ../../html-full/search/pages_12.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_7.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> ../../html-full/search/related_7.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> ../../html-full/search/search.css -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> ../../html-full/search/pages_1.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_b.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> ../../html-full/search/pages_b.js -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_26.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_104.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_26.svg -> ../html-full/inherit_graph_104.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_140.svg -> ../html-full/inherit_graph_598.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotSettings.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPlotSettings.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior.xhtml 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-> ../html-lib/optionfiletype_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000152_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> ../html-lib/dir_000152_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__inherit__graph.svg -> 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../html-lib/analysissettings_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__domdec__constraints__t.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__domdec__constraints__t.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__domdec__constraints__t.xhtml -> ../html-lib/structgmx__domdec__constraints__t.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_68.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_242.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_68.svg -> ../html-full/inherit_graph_242.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_38.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_147.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_38.svg -> ../html-full/inherit_graph_147.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbcenums_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> ../html-lib/pbcenums_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionListHandle-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle-members.xhtml -> ../html-full/structInteractionListHandle-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_205.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_962.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_205.svg -> ../html-full/inherit_graph_962.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_201.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_958.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_201.svg -> ../html-full/inherit_graph_958.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_16.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16.png -> ../html-full/form_16.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg -> ../html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000029_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000029_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000029_000002.xhtml -> ../html-full/dir_000029_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21.png -> ../html-full/form_34.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_53.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter__inherit__graph.svg -> ../html-full/classgmx_1_1IFrameConverter__inherit__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionsbehavior_8h__dep__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h__dep__incl.svg -> ../html-lib/ioptionsbehavior_8h__dep__incl.svg +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000081.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000074_000082.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000081.xhtml -> ../html-full/dir_000074_000082.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConvertTprInfo.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo.xhtml -> ../html-full/classgmx_1_1ConvertTprInfo.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000067_000007.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000007.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000067_000007.xhtml -> ../html-lib/dir_000068_000007.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter.xhtml -> ../html-full/classgmx_1_1IFrameConverter.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> ../html-full/classgmx_1_1MissingElementConnectionError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef__coll__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef__coll__graph.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_161.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_678.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_161.svg -> ../html-full/inherit_graph_678.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OutputRequirements-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements-members.xhtml -> ../html-full/structgmx_1_1OutputRequirements-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineparser_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h.xhtml -> ../html-lib/cmdlineparser_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000169.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000146_000170.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000169.xhtml -> ../html-full/dir_000146_000170.xhtml +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_189.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_934.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_189.svg -> ../html-full/inherit_graph_934.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> ../html-full/classgmx_1_1ElementNotFoundError-members.xhtml +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomentum-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum-members.xhtml -> ../html-full/structSystemMomentum-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals.xhtml -> ../html-lib/globals.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoption_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h.xhtml -> ../html-lib/selectionoption_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> ../html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000134_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000134_000002.xhtml -> ../html-full/dir_000135_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractdata_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractdata_8h__incl.svg -> ../html-full/abstractdata_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_28.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_106.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_28.svg -> ../html-full/inherit_graph_106.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1IsSerializableEnum-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1IsSerializableEnum-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1IsSerializableEnum-members.xhtml -> ../html-full/structgmx_1_1IsSerializableEnum-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_10_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10_dark.png -> ../html-full/form_10_dark.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection.xhtml -> ../html-lib/classgmx_1_1OptionSection.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> ../html-full/classgmx_1_1InvalidInputError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_j.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_j.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_j.xhtml -> ../html-full/namespacemembers_j.xhtml +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t-members.xhtml -> ../html-full/structgmx__ffparams__t-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_217.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1005.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_217.svg -> ../html-full/inherit_graph_1005.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter.xhtml -> ../html-full/classgmx_1_1IOutputAdapter.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gammadistribution_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> ../html-full/gammadistribution_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/repeatingsection_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> ../html-full/repeatingsection_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionManager__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionManager__inherit__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/programcontext_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h.xhtml -> ../html-lib/programcontext_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_91.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_356.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_91.svg -> ../html-full/inherit_graph_356.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t.xhtml -> ../html-full/structgmx__localtop__t.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Range-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Range-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Range-members.xhtml -> ../html-full/classgmx_1_1Range-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Range_1_1iterator.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator.xhtml -> ../html-full/structgmx_1_1Range_1_1iterator.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__inherit__graph.svg -> ../html-full/classgmx_1_1Int64Option__coll__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__inherit__graph.svg 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../html-full/classAtomProperties-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_179.svg -> ../html-full/inherit_graph_766.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__coll__graph.svg -> ../html-full/classgmx_1_1FileIOError__coll__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/timeunitmanager_8h__dep__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__dep__incl.svg -> ../html-lib/timeunitmanager_8h__dep__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignaller-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignaller-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignaller-members.xhtml -> ../html-full/classgmx_1_1SimulationSignaller-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties-members.xhtml -> ../html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> ../html-full/uniont__iparams-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_0.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0.png -> ../html-full/form_0.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000141_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000002.xhtml -> ../html-lib/dir_000141_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ITopologyProvider-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider-members.xhtml -> ../html-full/classgmx_1_1ITopologyProvider-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000169.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000093_000170.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000169.xhtml -> ../html-full/dir_000093_000170.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1RocfftPlan-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan-members.xhtml -> ../html-full/structgmx_1_1RocfftPlan-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nonbonded__bench_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h.xhtml -> ../html-lib/nonbonded__bench_8h.xhtml 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> ../html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_35_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22_dark.png -> ../html-full/form_35_dark.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21_dark.png -> ../html-full/form_34_dark.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/com_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h.xhtml -> ../html-lib/com_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__inherit__graph.svg -> ../html-full/classgmx_1_1FloatOption__coll__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.js -> ../../html-full/search/search.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/close.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/close.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/close.svg -> ../../html-full/search/close.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_9.js -> ../../html-lib/search/enums_9.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_14.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_14.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_14.js -> ../../html-lib/search/enumvalues_14.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_13.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_13.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_13.js -> ../../html-lib/search/enumvalues_13.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_15.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_15.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_15.js -> ../../html-full/search/enums_15.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1c.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1c.js -> ../../html-lib/search/all_1c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_9.js -> ../../html-lib/search/defines_c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag.svg -> ../../html-full/search/mag.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_d.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.js -> ../../html-lib/search/defines_d.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1a.js -> ../../html-lib/search/all_1c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_7.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_7.js -> ../../html-lib/search/defines_9.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_13.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_13.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_13.js -> ../../html-lib/search/typedefs_13.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_9.js -> ../../html-lib/search/enumvalues_9.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_4.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_4.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_4.js -> ../../html-lib/search/defines_4.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_seld.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_seld.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_seld.svg -> ../../html-full/search/mag_seld.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_0.js -> ../../html-full/search/defines_0.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.css -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.css -> ../../html-full/search/search.css +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1d.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1b.js -> all_1d.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_d.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_d.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_d.svg -> ../../html-full/search/mag_d.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_9.js -> ../../html-full/search/pages_c.js 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_f.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_f.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_f.js -> ../../html-full/search/enums_f.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_c.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_c.js -> ../../html-lib/search/enums_c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> ../../html-full/search/enums_13.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_4.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_4.js -> ../../html-full/search/pages_5.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_3.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_4.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_3.js -> ../../html-full/search/pages_4.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/classes_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_9.js -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_1.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> ../../html-lib/search/related_1.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_6.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.js -> ../../html-lib/search/defines_6.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/variables_a.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_a.js -> ../../html-lib/search/variables_a.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError-members.xhtml -> ../html-full/classgmx_1_1APIError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__coll__graph.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_31_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18_dark.png -> ../html-full/form_31_dark.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_5.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_10.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_5.svg -> ../html-full/msc_inline_mscgraph_10.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> ../html-lib/dir_000009_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/iframeconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iframeconverter_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/iframeconverter_8h__incl.svg -> ../html-full/iframeconverter_8h__incl.svg +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_221.svg -> ../html-full/inherit_graph_1031.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> ../html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision__coll__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_214.svg -> ../html-full/inherit_graph_1001.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_9.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_14.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_9.svg -> ../html-full/msc_inline_mscgraph_14.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000018_000019.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000018_000019.xhtml +changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPdbAtomEntry.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry.xhtml -> ../html-full/classPdbAtomEntry.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_10.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_15.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_10.svg -> ../html-full/msc_inline_mscgraph_15.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener-members.xhtml -> ../html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoption_8h__dep__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__dep__incl.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000084_000168.xhtml -> ../html-full/dir_000085_000169.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError-members.xhtml -> ../html-full/classgmx_1_1RangeError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_114.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_483.svg +changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpwriter_8h.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h.xhtml -> ../html-lib/cmdlinehelpwriter_8h.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput.xhtml -> ../html-full/classgmx_1_1LegacyInput.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000007.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000007.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000007.xhtml -> ../html-full/dir_000065_000007.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000093_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000002.xhtml -> ../html-lib/dir_000093_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000062.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000006_000063.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000062.xhtml -> ../html-lib/dir_000006_000063.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopend.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderopend.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopend.svg -> ../html-full/folderopend.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__incl.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_9_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9_dark.png -> ../html-full/form_9_dark.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000002.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000002.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000002.xhtml -> ../html-lib/dir_000146_000002.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork.xhtml -> ../html-lib/structgmx_1_1NbnxmPairlistCpuWork.xhtml +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000092.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000167_000093.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000092.xhtml -> ../html-lib/dir_000167_000093.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringCompare.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringCompare.xhtml -> ../html-full/classgmx_1_1StringCompare.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MappedUnionFinder.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder.xhtml -> ../html-full/classgmx_1_1MappedUnionFinder.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinemodule_8h__incl.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000008.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000171_000008.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000008.xhtml -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData.xhtml -> ../html-full/structgmx_1_1MDModulesWriteCheckpointData.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/average_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h__incl.svg -> ../html-full/average_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpueventsynchronizer_8h__incl.svg +changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_15_dark.png -> ../html-full/form_15_dark.png -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdmodulesnotifier_8h__incl.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> ../html-full/mdmodulesnotifier_8h__incl.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -> ../html-full/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_439.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_753.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_439.svg -> ../html-full/inherit_graph_753.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_42.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_103.svg -changed: 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-> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atominfo_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/atominfo_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atominfo_8h__incl.svg -> ../html-full/atominfo_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_143.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__excl__t.xhtml -> ../html-full/structgmx_1_1nbnxn__excl__t.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_51.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42.png -> ../html-full/form_51.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager-members.xhtml -> ../html-full/classgmx_1_1FileNameOptionManager-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_118.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_260.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_118.svg -> ../html-full/inherit_graph_260.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4.xhtml -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroupsCog-members.xhtml -> ../html-full/classgmx_1_1UpdateGroupsCog-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo-members.xhtml -> ../html-full/classgmx_1_1Int64OptionInfo-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000003.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000003.xhtml 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomRange.xhtml -> ../html-full/classAtomRange.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000144_000002.xhtml -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__sycl_8h.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h.xhtml -> ../html-full/gpuregiontimer__sycl_8h.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000170.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000170.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000170.xhtml -> ../html-full/dir_000111_000170.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -> ../html-full/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000170.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000009_000170.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000170.xhtml -> ../html-full/dir_000009_000170.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_22_dark.png +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22_dark.png -> ../html-full/form_22_dark.png +absolute: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> ../../html-full/search/search.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/close.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> ../../html-full/search/close.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_b.js -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_8.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> ../../html-full/search/groups_8.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_f.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_f.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_f.js -> ../../html-full/search/groups_f.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_7.js -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_seld.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_seld.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_seld.svg -> ../../html-full/search/mag_seld.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_5.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> ../../html-full/search/groups_5.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> ../../html-full/search/defines_0.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_e.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_e.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_e.js -> ../../html-full/search/groups_e.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> ../../html-full/search/groups_3.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enumvalues_13.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> ../../html-full/search/enumvalues_13.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_b.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> ../../html-full/search/groups_b.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_b.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> ../../html-full/search/pages_b.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> ../../html-full/search/search.css +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1d.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> all_1d.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_d.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> ../../html-full/search/mag_d.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_1.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> ../../html-full/search/pages_1.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_9.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_9.js -> ../../html-full/search/pages_9.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> ../../html-full/search/pages_c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_7.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> ../../html-full/search/pages_7.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_f.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_f.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_f.js -> ../../html-full/search/enums_f.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_1.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> ../../html-full/search/groups_1.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_19.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_19.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_19.js -> ../../html-full/search/functions_19.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_8.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> ../../html-full/search/related_8.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> ../../html-full/search/enums_13.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_a.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> ../../html-full/search/groups_a.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_4.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> ../../html-full/search/pages_4.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_3.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.js -> ../../html-full/search/pages_3.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_12.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> ../../html-full/search/pages_12.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> ../../html-full/search/pages_5.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_6.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> ../../html-full/search/groups_6.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_0.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> ../../html-full/search/pages_0.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_0.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_0.js -> ../../html-full/search/groups_0.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_8.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_a.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_8.js -> ../../html-full/search/defines_a.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_c.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> ../../html-full/search/related_c.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_d.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> ../../html-full/search/groups_d.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_sel.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> ../../html-full/search/mag_sel.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_7.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> ../../html-full/search/related_7.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_0.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_1.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_0.js -> ../../html-full/search/related_1.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_11.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_11.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_11.js -> ../../html-full/search/groups_11.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_d.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_e.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_d.js -> ../../html-full/search/pages_e.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_9.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> ../../html-full/search/related_9.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_10.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> ../../html-full/search/groups_10.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_a.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.js -> ../../html-full/search/enums_a.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_10.js -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_11.js +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_10.js -> ../../html-full/search/pages_11.js +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError-members.xhtml -> ../html-full/classgmx_1_1APIError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000033_000170.xhtml -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/math_2include_2gromacs_2math_2matrix_8h__incl.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/math_2include_2gromacs_2math_2matrix_8h__incl.svg -> ../html-full/math_2include_2gromacs_2math_2matrix_8h__incl.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -> ../html-full/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -absolute: 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../html-full/dir_a504950c834d58a27b0bd71a5abd3a11_dep.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ILogTarget-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ILogTarget-members.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ILogTarget-members.xhtml -> ../html-full/classgmx_1_1ILogTarget-members.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_6_dark.png -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_6_dark.png -changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMdpOptionProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IMdpOptionProvider-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMdpOptionProvider-members.xhtml -> ../html-full/classgmx_1_1IMdpOptionProvider-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggerBuilder-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder-members.xhtml -> 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+changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError-members.xhtml -> ../html-full/classgmx_1_1CheckpointError-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_426.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_740.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_426.svg -> ../html-full/inherit_graph_740.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_45.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_106.svg +changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_18.png -> ../html-full/form_18.png +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram-members.xhtml -> ../html-full/classgmx_1_1AbstractAverageHistogram-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpManager-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HelpManager-members.xhtml 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpLinks-members.xhtml -> ../html-full/classgmx_1_1HelpLinks-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> ../html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_454.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_770.svg 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/repeatingsection_8h.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h.xhtml -> ../html-lib/repeatingsection_8h.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlanSetupData.xhtml -changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData.xhtml -> ../html-lib/structgmx_1_1PlanSetupData.xhtml -absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool-members.xhtml -> ../html-full/classgmx_1_1Simd4FBool-members.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/read__params_8h__incl.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/read__params_8h__incl.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/read__params_8h__incl.svg -> ../html-full/read__params_8h__incl.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9223769e7949ef0e535eb89ee496ca73.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9223769e7949ef0e535eb89ee496ca73.xhtml +changed: 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/build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue.xhtml -> ../html-full/structPreprocessResidue.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000061.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000061.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000061.xhtml -> ../html-full/dir_000160_000061.xhtml +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg +absolute: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml +changed: /build/reproducible-path/gromacs-2025.3/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml dh_bash-completion -i dh_lintian -i dh_link -i @@ -396077,10 +68145,10 @@ dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a -dpkg-deb: building package 'gromacs' in '../gromacs_2025.3-1_amd64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2025.3-1_amd64.deb'. -dpkg-deb: building package 'libgromacs10' in '../libgromacs10_2025.3-1_amd64.deb'. +dpkg-deb: building package 'gromacs' in '../gromacs_2025.3-1_amd64.deb'. dpkg-deb: building package 'libgromacs10-dbgsym' in '../libgromacs10-dbgsym_2025.3-1_amd64.deb'. +dpkg-deb: building package 'libgromacs10' in '../libgromacs10_2025.3-1_amd64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2025.3-1_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2025.3-1_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2025.3-1_amd64.deb'. @@ -396092,12 +68160,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/141509/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3677769 and its subdirectories -I: Current time: Sat Nov 1 02:37:52 -12 2025 -I: pbuilder-time-stamp: 1762007872 +I: removing directory /srv/workspace/pbuilder/141509 and its subdirectories +I: Current time: Sat Dec 5 11:41:04 +14 2026 +I: pbuilder-time-stamp: 1796420464